5709a7858d5c197721be66d5218a79124abadb70 lrnassar Tue Mar 17 08:46:31 2026 -0700 Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 2540a710292..3061260ebe6 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -191,31 +191,31 @@ <a name="022426"></a> <h2>Feb. 24, 2026 Updates to the Genome Browser Gateway Page and Assembly Search</h2> <p> We are excited to announce new <b>Recent Genomes</b> and <b>Connected Hub Assemblies</b> lists on the <a href="/cgi-bin/hgGateway" target="_blank">Gateway page</a>, along with improvements to genome assembly searching across the Genome Browser. The genome assemblies search box is now also available on other pages and tools, including <a href="/cgi-bin/hgBlat" target="_blank">BLAT</a>, <a href="/cgi-bin/hgPcr" target="_blank">In-Silico PCR</a>, <a href="/cgi-bin/hgTables" target="_blank">Table Browser</a>, <a href="/cgi-bin/hgLiftOver" target="_blank">LiftOver</a>, <a href="/cgi-bin/hgCustom" target="_blank">Custom Tracks</a>, and others. </p> <div class="text-center"> -<img src="../../images/newsArchImages/gatewayLists.png" width='40%'> +<img alt="Screenshot of the UCSC Genome Browser gateway page with selectable genome assembly lists" src="../../images/newsArchImages/gatewayLists.png" width='40%'> </div> <p> <b>Recent Genomes:</b> Selected genomes are saved in the web browser and displayed in this list, with a maximum of 10 genomes stored. "UCSC Curated" genomes are maintained by UCSC with curated annotation tracks. "External" genomes are from connected track hubs. Clicking a card selects that genome on the Gateway page and displays its corresponding information. UCSC Curated genomes and public hub assemblies are searchable using the genome assemblies search box. The Recent Genomes list also appears in the blue navigation bar under Genomes, making it accessible throughout the Genome Browser for quick reuse. </p> <p> <b>Connected Hub Assemblies:</b> Track data hubs hosted outside of UCSC and currently connected to the Genome Browser are displayed in this list. To connect a hub, use the top blue bar and navigate to My Data > Track Hubs. @@ -330,31 +330,31 @@ <a href="/cgi-bin/hgTrackUi?db=mm10&position=default&g=recount3" target="_blank">mm10</a>. Recount3 is a comprehensive resource for re-analyzing RNA-seq data. It provides uniformly processed RNA-seq data and associated metadata from a wide range of studies, enabling researchers to access and analyze gene expression data in a consistent manner. Recount3 aggregates data from multiple sources, including the <a href="https://www.ncbi.nlm.nih.gov/sra/docs/" target="_blank">Sequence Read Archive (SRA)</a> and the <a href="https://commonfund.nih.gov/GTEx" target="_blank">Genotype-Tissue Expression (GTEx) project</a>, and reprocesses it using a standardized pipeline. This allows for cross-study comparisons and meta-analyses, facilitating discoveries in genomics and transcriptomics. </p> <p> The tracks display recount3 intron data, including split read counts and splice junction motifs. </p> <div class="text-center"> -<img src="../../images/newsArchImages/recount3.png" width='80%'> +<img alt="Browser display of the recount3 RNA-seq expression data track" src="../../images/newsArchImages/recount3.png" width='80%'> </div> <p> For hg38, the tracks available are: </p> <ul> <li>recount3 GTEx introns</li> <li>recount3 TCGA introns</li> <li>recount3 SRA introns</li> <li>recount3 CCLE introns</li> </ul> <p> For mm10: </p> <ul> @@ -377,56 +377,56 @@ <p> We would like to thank the ReCount team for making this data available. We would also like to thank Jeltje van Baren, Mark Diekhans, and Gerardo Perez for their efforts on this release. </p> <a name="020326a"></a> <h2>Feb. 03, 2026 New "Visible Tracks" group feature</h2> <p> We are excited to announce a new improvement to the UCSC Genome Browser: the <b>Visible Tracks</b> group. The Genome Browser now includes a dynamic track group that automatically displays all currently visible tracks in one convenient location. This means you no longer need to hunt through multiple track categories to adjust tracks you've already turned on. </p> <div class="text-center"> -<img src="/images/newsArchImages/visibleTracks.png" width='55%'> +<img alt="Screenshot showing the visible tracks shortcut feature in the Genome Browser toolbar" src="/images/newsArchImages/visibleTracks.png" width='55%'> </div> <p> Previously, managing visible tracks required navigating back to their original categories — whether that was Genes and Gene Predictions, Conservation, Variation, or any other group. Now, all your active tracks appear together in the <b>Visible Tracks</b> group, making it faster and easier to adjust display modes for visible tracks. </p> <p> The "Visible Tracks" group will appear only when more than 32 tracks are available for a genome assembly. </p> <p> We would like to thank Chris Lee and Jairo Navarro Gonzalez for releasing this feature.</p> <a name="020326b"></a> <h2>Feb. 03, 2026 Hub Space: Host Your Track Hubs Directly on the Genome Browser</h2> <p> We are excited to introduce <a href="/cgi-bin/hgHubConnect#hubUpload">Hub Space</a>, a new hosting service that enables users to upload and visualize track hub files directly on the UCSC Genome Browser without relying on third-party hosting services such as Dropbox, Google Drive, or AWS. </p> <div class="text-center"> -<img src="/images/newsArchImages/HubSpace.png" width='65%'> +<img alt="Screenshot of the HubSpace file hosting and track hub management interface" src="/images/newsArchImages/HubSpace.png" width='65%'> </div> <p> <b>Hub Space Features:</b><br> Each account is allocated 10 GB of storage space. While we strive to maintain uninterrupted access, please maintain your own backups. Data persistence over the long term is not guaranteed. To request additional storage space, please <a href="/contacts.html">contact us</a>. </p> <p> <b>How to Use Hub Space:</b><br> There are two primary ways to upload your files: </p> @@ -463,53 +463,53 @@ <a name="011526"></a> <h2>Jan. 15, 2026 New ENCODE cCREs track available for human (hg38)</h2> <p> We are proud to announce a new <a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=cCREs&position=default" target="_blank"> ENCODE Registry of cCREs (candidate Cis-Regulatory Elements)</a> container track for the hg38/GRCh38 genome as described in <a target="_blank" href="https://www.nature.com/articles/s41586-025-09909-9">Moore et al., <em>Nature</em> 2026</a>. This container contains candidate Cis-Regulatory Elements (cCREs) generated by the ENCODE Consortium during Phase 4 (ENCODE4) and Phase 3 (ENCODE3). The previous "ENCODE3 cCREs" track is retained for archival purposes. The tracks include both integrated (biosample-agnostic) and biosample-specific annotations derived from core epigenomic assays.</p> <div class="text-left"> <a href="https://genome.ucsc.edu/s/Lou/HBBexample" target=_blank> -<img src="/images/encode4cCREsNews.png" width='75%'></a> +<img alt="Announcement banner for ENCODE 4 candidate cis-regulatory elements" src="/images/encode4cCREsNews.png" width='75%'></a> </div> <p> The new tracks include:</p> <ul> <li><b><a href="/cgi-bin/hgTrackUi?c=chr7&g=cCREregistry&position=default&db=hg38" target="_blank"> ENCODE4 cCREs</a>:</b> This track presents the ENCODE Registry of 2,348,854 cCREs identified and classified using data from all phases of the ENCODE Project (Phases 1–4). The registry integrates chromatin accessibility and ChIP-seq signals across thousands of biosamples. All cCREs are consolidated into a single, cell type-agnostic annotation track displayed here.</li> <li><b><a href="/cgi-bin/hgTrackUi?c=chr7&g=coreCcres&position=default&db=hg38" target="_blank"> ENCODE4 Core Collection</a>:</b> This track displays biosample-specific cCREs alongside genome-wide epigenomic signals for the ENCODE4 Core Collection, consisting of 170 biosamples comprehensively profiled using four core assays: DNase-seq, ChIP-seq for H3K4me3 and H3K27ac (histone modifications), and ChIP-seq for CTCF. These data support detailed analysis of regulatory activity in individual biosamples.</li> </ul> <p> The cCREs are colored by their putative functional assignment based on biochemical signatures and genomic context:</p> <div class="text-left"> <p> -<img src="/images/encode4cCREs.png" width='35%'> +<img alt="Browser display of ENCODE 4 candidate cis-regulatory element tracks" src="/images/encode4cCREs.png" width='35%'> </div> <p> This results in the following classifications:</p> <table cellpadding='2'> <tr> <th style="border-bottom: 2px solid;">Color</th> <th style="border-bottom: 2px solid;"></th> <th style="border-bottom: 2px solid;">UCSC label</th> <th style="border-bottom: 2px solid;">ENCODE classification</th> <th style="border-bottom: 2px solid;">Classification criteria</th> </tr> <tr><td style='background-color: #FF0000;'> </td><td>red</td> <td>promoter</td> <td>promoter-like signature</td> @@ -713,86 +713,86 @@ </p> <a name="121525"></a> <h2>Dec. 15, 2025 Ancient Hominids track for hg38</h2> <p> We are happy to announce the release of the <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=ancient" target="_blank">Ancient Hominids track</a> featuring data from Archaic Sequence Hub (ArcSeqHub). This track shows variants identified by ArcSeqHub's remapping of high-quality Altai Neanderthal and Denisovan genomes onto the hg38/GRCh38 genome. Variants are divided into two subtracks, one for Denisovan variants and another for Neanderthal variants. UCSC has removed those positions from the VCF without an alternate allele to show only variants that are present in the ancient genomes.</p> <div class="text-center"> -<img src="/images/newsArchImages/ancientHominids.png" width='80%'></a> +<img alt="Browser display of ancient hominid variant tracks showing archaic human DNA differences" src="/images/newsArchImages/ancientHominids.png" width='80%'></a> </div> <p> We would like to thank the <a href="http://www.arcseqhub.com/plot/-1/" target="_blank">ArcSeqHub</a> authors for making the data available. We would also like to thank Maximilian Haeussler and Matthew Speir for the creation and release of this track.</p> <a name="120325"></a> <h2>Dec. 03, 2025 New gnomAD Missense Deleteriousness Prediction by Constraint (MPC) track for hg19</h2> <p> We are happy to announce the release of the <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=gnomadMpc" target="_blank">gnomAD Missense Deleteriousness Prediction by Constraint (MPC) track</a> for hg19, now available in the <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=gnomadSuper" target="_blank">gnomAD superTrack</a>. This track shows a score that tries to identify missense-depleted regions using the patterns of rare missense variation in 125,748 gnomAD v2.1.1 exomes, compared to a null mutational model. Missense-depleted regions are enriched for ClinVar pathogenic variants, de novo missense variants in individuals with neurodevelopmental disorders (NDDs), and complex trait heritability. This track can be used to aid in interpreting missense variants.</p> <p> Transcript regions with constraint predictions are colored using the viridis palette, where yellow indicates the lowest OE values and dark blue-purple indicates the highest.</p> <div class="text-center"> -<img src="../../images/newsArchImages/gnomAD_mpc.png" width='80%'></a> +<img alt="Browser display of the gnomAD missense pathogenicity constraint score track" src="../../images/newsArchImages/gnomAD_mpc.png" width='80%'></a> </div> <p> A corresponding MPC version for hg38 is planned for release by the gnomAD team in 2026.</p> <p> We would like to thank Kaitlin Samocha for suggesting this track and the <a href="https://gnomad.broadinstitute.org/about" target="_blank">Genome Aggregation Database Consortium (gnomAD)</a> for making the data available. We would also like to thank Maximilian Haeussler, Luis Nassar, and Gerardo Perez for the creation and release of this track.</p> <a name="111425"></a> <h2>Nov. 14, 2025 Updated Varaico Variants track and new Varaico Variants (suppl) track for hg38 and hg19</h2> <p> We are pleased to announce the release 2 of the <b>Varaico Variants track</b> and the addition of a new <b>Varaico Variants (suppl) track</b> for the human assemblies <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=varsInPubs" target="_blank">hg38/GRCh38</a> and <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=varsInPubs" target="_blank">hg19/GRCh37</a>. The Varaico tracks are generated using literature mining methods similar to those used for the <a href="http://bejerano.stanford.edu/AVADA/" target="_blank">AVADA</a> resource. With this update, the Varaico Variants track now contains more than 5.5 million variants.</p> <p> The Varaico Variants (suppl) track shows variants extracted from supplementary data files using similar methods to those used for the primary Varaico track.</p> <div class="text-center"> -<img src="../../images/newsArchImages/varaicoRelease2.png" width='80%'></a> +<img alt="Screenshot of the Varaico Release 2 clinical variant interpretation display" src="../../images/newsArchImages/varaicoRelease2.png" width='80%'></a> </div> <p> For more information, please visit the <a href="https://varaico.com/" target="_blank">Varaico website</a>.</p> <p> We would like to thank Johannes Birgmeier for generating and making the Varaico data available. We would also like to thank Maximilian Haeussler, Jairo Navarro Gonzalez, and Gerardo Perez for creating and releasing these tracks.</p> <a name="103125"></a> <h2>Oct. 31, 2025 New GENCODE "knownGene" V49 for human (hg38/hg19) and VM38 for mouse (mm39)</h2> <p> We are happy to announce the new GENCODE gene annotation tracks, corresponding to @@ -860,58 +860,56 @@ We are pleased to announce the release of the <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=spliceAIWt" target="_blank">SpliceAI Wildtype tracks</a> for hg38, available in the <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=spliceImpactSuper" target="_blank">Splicing Impact superTrack</a>. These tracks show the scores for the genome sequence itself, without variants, from predicted splice donor (5' intron boundaries) and splice acceptor (3' intron boundaries) sites. Predictions are strand-specific, with separate subtracks for the plus and minus strands. <ul> <li><b>SpliceAI Acceptor Plus</b> – Splice acceptor sites, plus strand <li><b>SpliceAI Acceptor Minus</b> – Splice acceptor sites, minus strand <li><b>SpliceAI Donor Plus</b> – Splice donor sites, plus strand <li><b>SpliceAI Donor Minus</b> – Splice donor sites, minus strand </ul> <p class="text-center"> -<img src="../../images/newsArchImages/spliceAIWildtype.png" -alt="SpliceAI Wildtype track display for the CFTR region" width='60%'></p> +<img alt="Browser display of SpliceAI variant pathogenicity prediction scores" src="../../images/newsArchImages/spliceAIWildtype.png" width='60%'></p> <p> These tracks are useful in combination with the variants track for evaluating new transcript models. They can be used to assess potential exon boundaries or possible splice acceptor sites.</p> <p> We would like to thank Illumina for making SpliceAI available, both the model and the precomputed data files. Thanks to Francois Lecoquierre from the University of Oxford, Jean-Madeleine de Sainte Agathe from Institut Pasteur Paris, and Michael Hiller from the Senckenberg Museum Frankfurt for suggesting and then creating the SpliceAI Wildtype annotations. We would also like to thank Max Haeussler and Gerardo Perez for their efforts on this release.</p> <a name="092525"></a> <h2>Sep. 25, 2025 Panmask Easy 151b Regions track for hg38</h2> <p> We are happy to announce the release of the <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=panmask151b" target="_blank">Panmask Easy 151b Regions</a> track for hg38. This new track is available in the <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=problematicSuper" target="_blank">Problematic Regions superTrack</a>. The track contains a set of sample-agnostic easy regions where short-read variant calling reaches high accuracy. Easy regions are derived for variant filtration agnostic to individual samples. They are genomic intervals where general variant callers achieve high accuracy without sophisticated filtering.</p> <p class="text-center"> -<img src="../../images/newsArchImages/panmask.png" -alt="Panmask Easy 151b Regions track for the BRCA1 exon 19" width='75%'></p> +<img alt="Browser display showing pangenome masking tracks for repetitive regions" src="../../images/newsArchImages/panmask.png" width='75%'></p> <p> The pm151 regions are used to filter spurious variant calls in centromeres, long repeats, and other genomic regions where short-read mapping is often problematic. They cover 88.2% of hg38, 92.2% of coding regions, and 96.3% of ClinVar pathogenic variants. The track can be used to filter variant calls for clinical or research human samples. It shows regions that are easy to sequence, rather than those that are problematic. The data was derived from the HPRC assemblies, and this track presents the 151b-easy panmask set.</p> <p> We would like to thank <a href="https://hlilab.github.io/" target="_blank">Heng Li's group</a> at Harvard Medical School for making this data available. We would also like to thank Max Haeussler and Gerardo Perez for their efforts on this release.</p> <a name="092425"></a> <h2>Sep. 24, 2025 CoLoRSdb small and structural variants for hg38 and hs1</h2> @@ -924,32 +922,31 @@ discovered through long-read whole genome sequencing, contributed by the international <a href="https://colorsdb.org" target="_blank">Consortium of Long Read Sequencing (CoLoRS)</a>. The small variant tracks (DeepVariant + GLnexus) contain single nucleotide polymorphisms (SNPs) and short indels, while the structural variant tracks (pbsv + Jasmine) display larger events including insertions, deletions, and inversions. Long-read sequencing technology improves sensitivity in repetitive regions and provides more precise breakpoint resolution than short-read approaches, enabling accurate visualization of complex loci in the Genome Browser.</p> <p> Each track includes allele frequency and sample count annotations, with additional filtering options for variant size and type. Users can click on individual variants to view detailed metadata, such as allele counts, homozygous/heterozygous call distributions, and Hardy-Weinberg equilibrium values. </p> <div class="text-center"> <a href="https://genome.ucsc.edu/s/jnavarr5/CoLoRSdb_announcement"> - <img src="../images/newsArchImages/CoLoRSdb.png" - alt="CoLoRSdb track with the mouseover tooltip on the DEL-159bp item." width='65%'> + <img alt="Browser display of CoLoRSdb structural variant tracks from long-read sequencing" src="../images/newsArchImages/CoLoRSdb.png" width='65%'> <p class="gbsCaption"> <em>Genome Browser screenshot of the CoLoRSdb tracks with the mouseover tooltip on the DEL-159bp item.</em> </p></a> </div> <p> We would like to thank Mike Schatz, Evan Eichler, and all <a href="https://colorsdb.org/membership" target="_blank">CoLoRSdb investigators</a> for generating and making the data publicly available. We would also like to thank Karen Wang and Jairo Navarro Gonzalez for the creation and release of these tracks. </p> <a name="091925"></a> <h2>Sep. 19, 2025 Developmental Disorders Gene2Phenotype (DDG2P) for hg38 and hg19</h2> <p> @@ -976,61 +973,59 @@ <ul> <li><strong>G2P ID</strong>: Unique identifier assigned by the Gene2Phenotype (G2P) database.</li> <li><strong>Variant Consequence</strong>: Predicted effect each allele of a variant has on a transcript.</li> <li><strong>Disease Name</strong>: Name of the disease associated with the variant.</li> <li><strong>PubMed IDs</strong>: Publications associated with the variant.</li> <li><strong>Molecular Mechanism</strong>: Description of the molecular processes and interactions causing pathogenic effects.</li> <li><strong>Allelic Requirements</strong>: Number of alleles required at a locus to produce a pathogenic phenotype (e.g., monoallelic, biallelic).</li> <li><strong>Date of Last Review</strong>: Most recent date the entry was manually reviewed.</li> </ul> <div class="text-center"> <a href="https://genome.ucsc.edu/s/jnavarr5/ddg2p_announcement"> - <img src="../images/newsArchImages/ddg2p.png" - alt="DDG2P track with the mouseover tooltip on the BRCA1 gene." width='75%'> + <img alt="Browser display of developmental disorder gene-to-phenotype tracks" src="../images/newsArchImages/ddg2p.png" width='75%'> <p class="gbsCaption"> <em>Genome Browser screenshot of the DDG2P track with the mouseover tooltip on the BRCA1 gene.</em> </p></a> </div> <p> We would like to thank the <a href="https://www.ebi.ac.uk/gene2phenotype/about/project" target="_blank">G2P project</a> for making this data publicly available. We would also like to thank Jaidan Jenkins-Kiefer and Jairo Navarro Gonzalez for the creation and release of the Genome Browser tracks.</p> <a name="082125"></a> <h2>Aug. 21, 2025 MaveDB Experiment Heatmaps and Alignment track for hg38</h2> <p> We are excited to announce the release of the <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=mavedb_maps">MaveDB Experiment Heatmaps and Alignment</a> track for hg38. This release provides heatmaps of <b>m</b>ultiplexed <b>a</b>ssays of <b>v</b>ariant <b>e</b>ffects (MAVE) from <a target="_blank" href="https://mavedb.org/">MaveDB</a>. Each heatmap presents the results of an experiment where many small substitutions were tested within a gene to examine their functional consequences. Accompanying tracks display alignments of each experiment sequence to the genome. </p> <p> Please note that only a subset of MaveDB experiments could be displayed as heatmaps; the sequence alignments in this track only cover those experiments.</p> <div class="text-center"> <a href="https://genome.ucsc.edu/s/view/MaveDB_BRCA1"> - <img src="../images/newsArchImages/MaveDB_BRCA1_exon_19.png" - alt="MaveDB heatmap and alignment tracks for the BRCA1 exon 19" width='75%'> + <img alt="Browser display of MaveDB BRCA1 variant effect map scores" src="../images/newsArchImages/MaveDB_BRCA1_exon_19.png" width='75%'> <p class="gbsCaption"> <em>Genome Browser screenshot of BRCA1 exon 19 showing the alignment and heatmap tracks.</em> </p></a> </div> <p> Hover over each item in the heatmap to see the consequence of substituting individual amino acids within the genome with alternatives. Score ranges vary among experiments, but each is presented with the highest scores in <span style="color: #FF0000; font-weight: bold;">red</span>, the lowest scores in <span style="color: #0000FF; font-weight: bold;">blue</span>, and scores at the midpoint between the two in <span style="color: #C0C0C0; font-weight: bold;">silver</span>. Higher scores correspond to a higher enrichment level for that variant compared to others in the experiment set. </p> <p> We would like to thank Jeremy Arbesfeld and the MaveDB team for making this data publicly available. We would also like to thank Melissa Cline, Jonathan Casper, and Jairo Navarro for the @@ -1076,31 +1071,31 @@ available in the PanelApp composite track. The PanelApp track shows expert, crowdsourced diagnostic disease panels among genes, copy-number variants (CNV), and short tandem repeats (STR). PanelApp Australia was originally launched by <a href="https://www.australiangenomics.org.au/tools-and-resources/panelapp-australia/" target="_blank">Australian Genomics</a> in 2019 in collaboration with <a href="https://panelapp.genomicsengland.co.uk/" target="_blank">Genomics England</a> and is currently supported by Genomics Australia. The PanelApp Australia track contains data that differs from the Genomics England PanelApp; more details are available on the <a href="/cgi-bin/hgTrackUi?db=hg38&g=panelApp&position=default#TRACK_HTML" target="_blank">track description page.</a> <p> We have also updated the mouse hover for the Genomics England PanelApp track, which now shows the gene name, associated panel, mode of inheritance (if known), related phenotypes, and confidence level.</p> <div class="text-center"> - <img src="../images/panelAppAustralia.jpg" width='80%'></a> + <img alt="Browser display of PanelApp Australia gene panel diagnostic tracks" src="../images/panelAppAustralia.jpg" width='80%'></a> </div> <p> We want to thank Jean-Madeleine for this data request and feedback, as well as Zornitza Stark from Australia PanelApp for providing guidance. We would also like to thank Beagan Nguy, Lou Nassar, and Gerardo Perez of the Genome Browser team for the development and release of this track.</p> <a name="080125"></a> <h2>Aug. 01, 2025 PubTator Variants track for human, hg38 and hg19</h2> <p> We are excited to announce the release of the PubTator Variants track for human assemblies, <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=pubtator">hg38</a> and <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=pubtator">hg19</a>. These tracks were created using PubTator3 data and are freely accessible to the research community. PubTator3 is a web-based system that offers a comprehensive set of features and tools that allow researchers to explore biomedical literature for knowledge discovery. It uses @@ -1120,31 +1115,31 @@ methylation data: <a href="https://www.encodeproject.org/data-standards/wgbs/" target="_blank">bedMethyl</a>. This format, and its binary-indexed counterpart, <b>bigMethyl</b>, is designed to represent methylation calls from bisulfite sequencing or similar methods at single-base resolution across the genome.</p> <p> The <a href="help/bedMethyl.html" target="_blank">bedMethyl</a> format extends the standard <a href="/FAQ/FAQformat.html#format1" target="_blank">BED 9 format</a> to include additional fields such as coverage, percent methylation, and the number of modified and canonical bases. When viewed in the Genome Browser, hovering over or clicking an item reveals these additional details. Items are color-coded from <b><font color="#0000FF">0%</font></b> methylated (blue) to <b><font color="#FF0000">100%</font></b> (red). Methylation calls are shown separately for CpG sites (<b>m</b>) and non-CpG (CHG/CHH) sites (<b>h</b>). </p> <p class="text-center"> -<img "1080" height="148" src="../../images/bedMethylEx.jpg"> +<img "1080" height="148" alt="Browser display of a bedMethyl DNA methylation data track" src="../../images/bedMethylEx.jpg"> </p> <p> The <a href="help/bedMethyl.html#bigMethyl" target="_blank">bigMethyl</a> format allows fast access to large methylation datasets and is ideal for displaying these tracks at scale in the Genome Browser.</p> <p> For more information, see the <a href="help/bedMethyl.html" target="_blank">bedMethyl and bigMethyl Track Format</a> help page. </p> <p> We would like to thank Brian Joseph Raney, Max Haeussler, and Gerardo Perez for their work developing and testing this track format.</p> </p> <a name="072325"></a> @@ -1203,32 +1198,31 @@ <h2>July 15, 2025 ENCODE4 Long-read RNA-seq Transcripts</h2> <p> We are pleased to announce the release of the ENCODE4 long-read RNA-seq transcripts track for <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=encode4LongRnaTranscripts" target="_blank">hg38</a> and <a href="/cgi-bin/hgTrackUi?db=mm10&position=default&g=encode4LongRnaTranscripts" target="_blank">mm10</a>. This track annotates transcripts using numerical triplets representing the identity of the start site, exon junction chain, and transcript end site of each transcript. This is presented alongside sample enrichment information to show how promoter selection, splice pattern, and 3’ processing are deployed across human tissues. </p> <div class="text-center"> - <img src="../images/encode4LongReadTranscriptsHelp.png" - alt="Screenshot showing ENCODE4 long-read transcripts track"> + <img alt="Browser display of ENCODE 4 long-read RNA transcript annotations" src="../images/encode4LongReadTranscriptsHelp.png"> </div> <p> Transcripts are labeled with triplets, e.g. [1,1,1] or [1,1,3] or [2,1,3]. If transcripts share a number in any of the positions that means they share that feature, e.g. sharing a 8 in the second position but different numbers in the others means those two transcripts share the same set of exons, but different start and end sites. </p> <p> This track is part of a "Long-read Transcripts" supertrack that will consist of other datasets derived from third-generation sequencing technology, such as PacBio and Oxford Nanopore. </p> @@ -1572,31 +1566,31 @@ "<b>Va</b>riation <b>R</b>esearch <b>A</b>dvancing <b>I</b>nsight in <b>C</b>omplex <b>O</b>rganisms". Varaico was created using literature mining, similar to AVADA. </p> <p> Varaico variants are generated by an automated process that extracts purely factual information about genes from scientific papers (by matching strings against gene names) and HGVS variant descriptions (using regular expressions). Varaico aims to reduce false-positive gene and variant mentions and link them together appropriately, but nonetheless, many variants displayed are not mapped to the genomic position intended by the authors. Visit the <a href="https://varaico.com/" target="_blank">Varaico website</a> for more details.</p> <p> Mouse over the variants to show the gene, variant, latest author/year/title, number of publications mentioning the variant, and variant effect. Varaico variants may or may not be disease-causing.</p> <div class="text-center"> - <img src="../images/newsArchImages/Varaico.png" width="80%"> + <img alt="Screenshot of the Varaico clinical variant browser interface" src="../images/newsArchImages/Varaico.png" width="80%"> <p class="gbsCaption"> <em>Mouse-over is shown for the orange item (BRCA1 c.4136_4137del).</em> </p> </div> <p> We would like to thank Johannes Birgmeier for generating and making the Varaico data available. We would also like to thank Maximilian Haeussler and Jairo Navarro Gonzalez for creating and releasing these tracks. </p> <a name="051925"></a> <h2>May 19, 2025 New GENCODE "knownGene" V48 for human (hg38/hg19) and VM37 for mouse (mm39)</h2> <p> We are pleased to announce the release of the GENCODE Genes V48 for human @@ -1683,32 +1677,31 @@ expression levels across 50 tissues from the Genotype Tissue Expression (GTEx) v10 dataset, showing a comprehensive view of the expression of exons across a gene using the proportion expression across transcripts, or pext metric, a transcript-level annotation metric which quantifies isoform expression for variants. </p> <p> This is especially useful for those interested in alternative splicing and clinical assessment of variants. For more information, see the <a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadPext" target="_blank">track description page</a> and the <a href="https://www.nature.com/articles/s41586-020-2329-2" target="_blank">associated publication</a>.</p> <div class="text-center"> - <a href="https://genome.ucsc.edu/s/Lou/hg38pextNews" target="_blank"><img src="../images/hg38pextTrackNewsImage.png" -alt="Image of TRDN gene showing variants primarily expressed in heart tissue." width='80%'></a> + <a href="https://genome.ucsc.edu/s/Lou/hg38pextNews" target="_blank"><img alt="Browser display of hg38 patch extension tracks with sequence alignments" src="../images/hg38pextTrackNewsImage.png" width='80%'></a> </div> <p> We would like to thank the gnomAD team and the UCSC Genome Browser team members Jeltje van Baren, Max Haeussler, Lou Nassar, and Anna Benet-Pages for developing and releasing this track, as well as making the Exon Relevance RTS. </p> <a name="050525"></a> <h2>May 5, 2025 VISTA Enhancers track update for Human and Mouse</h2> <p> We are happy to announce an update to the VISTA Enhancers tracks for human (<a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=vistaEnhancersBb">GRCh38/hg38</a> and <a target="_blank" @@ -1905,32 +1898,31 @@ all items with a score of 300 or above.</p> <pre> highlightText.name NM* </pre> <p> The example above uses the <code>highlightText</code> setting, which will apply a highlight on the field <code>name</code>. Using this setting, any items that begin with <i>NM</i> are highlighted.</p> <pre> highlightColor #ff0000 </pre> <p> In this final example, the <code>highlightColor</code> is used to set the default highlight color. With this setting, all highlight stripes will use the color red, <code>#ff0000</code>.</p> <div class="text-center"> - <img src="../images/newsArchImages/highlightAnnouncement.png" - alt="Items in the NCBI RefSeq Historical track that begin with NM are highlighted red."> + <img alt="Screenshot showing the track highlight feature for emphasizing genomic regions" src="../images/newsArchImages/highlightAnnouncement.png"> <p>Items in the NCBI RefSeq Historical track for hg38 have all items that begin with "NM" highlighted in red.</p> </div> <p> We would like to thank Chris Lee and Jairo Navarro for their efforts in creating and testing the highlight feature for track hubs.<p> <a name="022425"></a> <h2>Feb. 24, 2025 enGenome VarChat track for human (hg38 and hg19)</h2> <p> We are happy to announce the release of the enGenome VarChat track for the <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=varChat&position=default" >hg38/GRCh38</a> and <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg19&g=varChat&position=default">hg19/GRCh37</a> human assemblies, available in the Variants in Papers superTrack. @@ -2068,31 +2060,31 @@ target="_blank">Dog (canFam6)</a>, and <a href="/cgi-bin/hgTrackUi?db=danRer11&g=refSeqComposite&position=default" target="_blank">Cow (bosTau9)</a> assemblies. This track shows orthologous genes across genomes and allows you to explore gene symbols and orthology information by hovering over or clicking on the track item, with links to the corresponding genome browsers:</p> <div class="text-center"> <a href="https://genome.ucsc.edu/s/gperez2/hg38_NCBI_ortholog_track" target="_blank"> <img src="../images/newsArchImages/ortholog_track.png" alt="hg38 session visualizing the NCBI Gene Orthologs track" width='50%'></a> </div> <p> You can find the NCBI Orthologs track within the NCBI RefSeq composite track:</p> <div class="text-center"> - <img class='text-center' width="50%" src="../../images/newsArchImages/ortholog_refSeq.png"> + <img class='text-center' width="50%" alt="Browser display of orthologous RefSeq gene annotations mapped across species" src="../../images/newsArchImages/ortholog_refSeq.png"> </div> <p> This track was created using the latest <a href="https://ftp.ncbi.nih.gov/gene/DATA/" target="_blank">NCBI files</a> (gene2accession and gene_orthologs). More information on this track can be found on the <a href="/cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite#TRACK_HTML" target="_blank">track description</a> page.</p> <p> We would like to thank <a href="https://www.ncbi.nlm.nih.gov/" target="_blank">NCBI</a> for making this data available. We would also like to thank Jeltje van Baren, Mark Diekhans, Max Haeussler, and Gerardo Perez for the creation and release of this track. </p> @@ -2279,31 +2271,31 @@ tab-separated files. We would also like to thank Jeltje van Baren, Lou Nassar, and Gerardo Perez for the creation and release of these tracks.</p> <a name="100124"></a> <h2>Oct. 1, 2024 New interactive variant interpretation tutorial</h2> <p> We have a new <a href="/cgi-bin/hgTracks?db=hg38&startClinical=true" target="_blank">clinical tutorial</a> showcasing resources that could be useful in variant interpretation. The tutorial is written to educate clinical geneticists with any level of browser experience. It covers topics such as searching for variants and data, recommended track sets, and how to save and share browser configurations.</p> <p> <div class="text-center"> <a href="/cgi-bin/hgTracks?db=hg38&startClinical=true" target="_blank"> - <img src="/images/clinicalTutorial.png" width='30%'> + <img alt="Thumbnail for the clinical genomics tutorial showing Genome Browser usage" src="/images/clinicalTutorial.png" width='30%'> </a> </div> </p> <p> We would like to thank Jairo Navarro, Chris Lee, Anna Benet-Pages, Maximilian Haeussler and Lou Nassar for their work in creating this tutorial.</p> <a name="093024"></a> <h2>Sep. 30, 2024 New gnomAD v4.1 tracks for hg38</h2> <p> We are excited to release six new <a target=_blank href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadVariants"> Genome Aggregation Database (gnomAD) v4.1 tracks</a> for human assembly hg38/GRCh38. The new tracks are found in the gnomAD superTrack:</p> @@ -2475,65 +2467,65 @@ <p> We would like to thank Chris Lee, Jairo Navarro, and Lou Nassar for their work on this release.</p> <a name="082124"></a> <h2>Aug. 21, 2024 New groups feature for track hubs</h2> <p> We are excited to announce a new grouping feature for track hubs, which allows the structured organization of tracks into distinct groups. This feature can be applied to a UCSC genome, a GenArk assembly, or an assembly hub. These track hub groups are kept separate from other track hubs and the native UCSC Genome Browser track groups, allowing for greater organizational flexibility. For instance, you can add a "genes" group without causing conflicts or confusion. You can define groups with names like "Category 1", "Category 2", and "Category 3". <div class="text-center"> - <img class='text-center' width="80%" src="../../images/groupsEx.png"> + <img class='text-center' width="80%" alt="Screenshot showing track hub group organization and category display" src="../../images/groupsEx.png"> </div> <p> For more information, see the <a href="/goldenPath/help/hgTrackHubHelp.html#Group" target="_blank">Adding Groups to a Track hub</a> section of the Track Hubs help page.</p> <p> We would like to thank Brian Joseph Raney, Mark Diekhans, Luis Nassar, and Gerardo Perez for their work on this release.</p> <a name="081424"></a> <h2>Aug. 14, 2024 New pop-up dialogue box for item details</h2> <p> We are excited to introduce the new Item Details feature which simplifies the user experience by displaying track item details in a pop-up dialogue box. This feature allows the information to be viewed without the need to navigate away from the current page:</p> <div class="text-center"> - <img class='text-center' width="60%" src="../../images/ItemDetails_knownGene.png"> + <img class='text-center' width="60%" alt="Item details popup displaying gene information for a UCSC Known Gene entry" src="../../images/ItemDetails_knownGene.png"> </div> <p> When a track item is clicked in either pack or full mode, the <b>Item Details</b> dialogue box will appear. This box can be resized by clicking and dragging the button located in its lower-right corner. For users who prefer viewing item details on a separate page, clicking the new window button in the upper-right corner will load the information in a new tab. The dialogue box can be closed by clicking the <b>x</b> button, the <button type="button">Close</button> button, pressing the Escape key, or by clicking outside the box.</p> <p> If desired, this feature can be disabled by unchecking the "Enable pop-up when clicking items option" on the Configure page. You can access the Configure page by selecting Configure under Genome Browser in the blue bar menu, by clicking the <button type="button">Configure</button> button below the browser graphic, or by using the keyboard shortcut "c f".</p> <div class="text-center"> - <img class='text-center' width="30%" src="../../images/configure_ItemDetails.png"> + <img class='text-center' width="30%" alt="Configuration panel for customizing item details display settings" src="../../images/configure_ItemDetails.png"> </div> <p> We would like to thank Christopher Lee, Lou Nassar, Jairo Navarro, and Gerardo Perez for their work on this release.</p> <a name="081224"></a> <h2>Aug. 12, 2024 Illumina SpliceAI tracks for human (hg38 and hg19)</h2> <p> We are pleased to announce the release of the <b>Illumina SpliceAI</b> tracks for the <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=spliceAI" target="_blank">hg38</a> and <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=spliceAI" target="_blank">hg19</a> human assemblies. SpliceAI is an <a href="https://github.com/Illumina/SpliceAI" target="_blank">open-source</a> deep learning splicing prediction algorithm that can predict splicing alterations caused by DNA variations. Such variants may activate nearby cryptic splice sites, leading to abnormal transcript @@ -3436,61 +3428,61 @@ other locations of the genome (off-target effects). Efficiency is the frequency of cleavage at the target site (on-target efficiency).</p> <p> We would like to thank Maximilian Haeussler, Hiram Clawson, and Gerardo Perez for developing and releasing these tracks.</p> <a name="110823"></a> <h2>Nov. 08, 2023 New track decorators feature</h2> <p> We are excited to introduce the new track decorators feature which allows highlighting parts of features with colors and/or symbols (glyphs/shapes) within a single track. </p> <div class="text-center"> <a href="http://genome.ucsc.edu/s/gperez2/RM_32467" target="_blank"> - <img src="../images/newsArchImages/feature_decorators.png" style="width:80%;max-width:1083px"></a> + <img alt="Gene track with colored block decorators highlighting protein domains" src="../images/newsArchImages/feature_decorators.png" style="width:80%;max-width:1083px"></a> </div> <p> The genome browser‘s primary way to annotate the genome uses colored rectangles (“exons” for gene tracks) linked by thin lines (“introns”), often stored as a bigBed. These were originally used for genes but then evolved to cover other types of annotations, e.g. enhancers, chromatin modifications, or single nucleotide variants. We usually call these annotations “features”. Each rectangle (“exon”) of a feature has the same color and individual parts cannot be highlighted. If you wanted to highlight parts of the features, traditionally this required a second track. </p> <div class="text-center"> - <img src="../../images/runx2.png" style="width:80%;max-width:1083px"> + <img alt="RUNX2 gene region with standard gene annotations" src="../../images/runx2.png" style="width:80%;max-width:1083px"> </div> <p> Track decorators change this: in your custom track and track hubs, you can now highlight parts of a genome annotation with colors or symbols. Track decorators can be shown in two styles, “block” and “glyph” style, and can either be overlaid onto the feature or shown directly underneath. The “block” style option can be used to color exons and introns and can display a label for them. For example, the “block” track decorator could be used to overlay protein domain boundaries on transcripts where usually one would use an entirely different track for the domains. </p> <div class="text-center"> - <img src="../../images/runx2_decorator.png" style="width:80%;max-width:1083px"> + <img alt="RUNX2 gene region with Pfam protein domain decorator overlays" src="../../images/runx2_decorator.png" style="width:80%;max-width:1083px"> </div> <p> The “glyph” style option offers 8 different types of glyphs and the color of choice. </p> <div class="text-center"> - <img src="../../images/glyphsEx.png" style="width:40%;max-width:1083px"> + <img alt="Reference chart of available decorator glyph shapes" src="../../images/glyphsEx.png" style="width:40%;max-width:1083px"> </div> <p> The “glyph” style option can be used to draw entirely new symbols, for example, to indicate insertion positions on the genome with small triangles. For more information, see the <a href="/goldenPath/help/decorator.html" target="_blank">Track Decorators help page</a>.</p> <p> We would like to thank Jonathan Casper, Max Haeussler, Mark Diekhans, and Gerardo Perez for their work on this release. We appreciate user feedback. If you have questions, feedback, suggestions, glyph style requests, or have found new glyph applications, please contact our <a href="mailto:genome@soe.ucsc.edu">mailing list</a>. We would appreciate responses on the creative ways of using the new track decorators feature. </p> <a name="102323"></a> <h2>Oct. 23, 2023 eMERGE polygenic risk scores for human (hg19)</h2> @@ -3716,45 +3708,45 @@ release of these tracks.</p> <a name="080723"></a> <h2>Aug. 07, 2023 Introducing an interactive tutorial for the UCSC Genome Browser</h2> <p> We are happy to announce the release of a new interactive tutorial for the UCSC Genome Browser. The tutorial is designed to help new users navigate the UCSC Genome Browser. Topics such as navigating around the Genome Browser display, configuring track display settings, searching for tracks, and viewing the negative strand (3' to 5') are covered in the tutorial.</p> <p> To begin the tutorial, select the <em>Interactive tutorial</em> from the "Help" drop-down menu. <div class="text-center"> <a href="/cgi-bin/hgTracks?db=hg38&position=default"> - <img src="/images/newsArchImages/hgTracksTutorial.png" width="900"> + <img alt="Thumbnail for the hgTracks Genome Browser navigation tutorial video" src="/images/newsArchImages/hgTracksTutorial.png" width="900"> </a> </div> </p> <p> We would like to thank Chris Lee and Jairo Navarro for their work in creating this tutorial.</p> <a name="080123"></a> <h2>Aug. 01, 2023 New ability to create duplicate tracks</h2> <p> We are pleased to announce the new Duplicate track feature, which allows a copy of a track to have its own independent settings and be used for multiple display views.</p> <div class="text-center"> <a href="http://genome.ucsc.edu/s/gperez2/RM_30365" target="_blank"> - <img src="../images/duplicateDisplay.png" width="300"></a> + <img alt="Screenshot demonstrating the duplicate track display feature" src="../images/duplicateDisplay.png" width="300"></a> </div> <p> You can have multiple duplicates of the same track where the number will increment by one for each additional duplicate, and each duplicated track is independent of each other. Only tracks that are not inside of composite or supertracks can be duplicated and this feature does not work in hubs.</p> <p> Duplicate tracks can be helpful when comparing different settings and visibility types on the same data; for instance, displaying all GENCODE genes, including pseudogenes, in dense mode, alongside a more concise gene set, such as the default, in pack mode to see gene symbols and accessions. This is shown in the image below, where duplicated GENCODE track has the additional text "(duplicate #1)" on the label above the track display and "#1" text on the left label of the track display.</p> <div class="text-center"> <a href="http://genome.ucsc.edu/s/gperez2/RM_30365_v2" target="_blank"> @@ -4913,32 +4905,31 @@ href="https://www.gencodegenes.org/pages/gencode.html">GENCODE project</a> for providing these annotations. We would also like to thank Mark Diekhans and Lou Nassar for the development and release of these tracks.</p> <a name="050522"></a> <h2>May 5, 2022 Merged Cell Expression on hg38</h2> <p> The Genome Browser already provided <a href="#111721">single-cell RNA-seq datasets</a> for the human GRCh38/hg38 assembly, but those data have so far been split among a collection of tracks depending on the organ and publication source. We are happy to announce that data from 12 of those papers (and 14 organs) are now available in a combined <a href="../cgi-bin/hgTrackUi?db=hg38&g=singleCellMerged">Merged Cells</a> track that provides normalized RNA-seq values for every cell type in those sets. All components were normalized to show expression in parts per million.</p> <figure class="text-center"> -<img src="../images/singleCell/singleCellMerged.png" style="width: 80%; max-width: 1318px;" -alt="Example of the Merged Cells track display for the ACE2 gene"> +<img alt="Browser display of merged single-cell RNA-seq expression across cell types" src="../images/singleCell/singleCellMerged.png" style="width: 80%; max-width: 1318px;"> </figure> <p> The following tracks were incorporated into this Merged Cells track: <ul> <li> <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=bloodHao&position=default">Blood (PBMC) Hao</a> </li> <li> <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=colonWang&position=default">Colon Wang</a> </li> <li> <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=cortexVelmeshev&position=default">Cortex Velmeshev</a> @@ -5468,49 +5459,49 @@ <a name="022222"></a> <h2>Feb. 22, 2022 Recommended Track Sets paper</h2> <p> We are pleased to announce a new paper about our Recommended Tracks Set feature, available on GRCh37/hg19, which collects related clinical tracks to help investigate variants. The paper, <a href="https://doi.org/10.1002/humu.24335" target="_blank">Variant interpretation: UCSC Genome Browser Recommended Track Sets</a>, covers how this new feature can facilitate the interpretation of variants for clinicians.</p> <p> Track Sets allow a user to quickly swap out the on-screen annotations they may be looking at for a different set of tracks relevant to specific medical scenarios: investigating single nucleotide variants in coding regions (Clinical SNVs), structural copy number variants (Clinical CNVs), and functional aspects of non-coding variants (Non-coding SNVs).</p> <p class ="text-center"> <a href="https://doi.org/10.1002/humu.24335"> - <img class="text-center" src="../images/newsArchImages/track_sets1.png" width="900px"> + <img class="text-center" alt="Screenshot of the recommended track sets feature for quick track configuration" src="../images/newsArchImages/track_sets1.png" width="900px"> </a> </p> <p> To access Recommended Track Sets, currently available only on the hg19 assembly, go to the top blue bar and under the "Genome Browser" menu click the "Recommended Track Sets" option. This will launch a dialog box offering pre-configured track sets, enabling swapping from one view to another view without changing the current position. Please note this figure does not include a fourth Track Set, Problematic Regions, we added since the release of the paper. Problematic Regions help users evaluate if annotations in the Browser are located in areas of the genome of low confidence due to high homology or other reported concerns. Once displayed, Recommended Track Sets can then be customized, where one can configure tracks in the browser by clicking the grey bar on the left of a track. Or to see more information about displayed items, one can mouseover for an informative pop-up summary, or click on the item to access a details page.</p> <p> The paper gives an example of using the experimental data in the Clinical SNV Track Set to examine a variant.</p> <p class ="text-center"> <a href="https://doi.org/10.1002/humu.24335"> - <img class="text-center" src="../images/newsArchImages/track_sets2.png" width="900px"> + <img class="text-center" alt="Track sets selection interface showing available predefined track collections" src="../images/newsArchImages/track_sets2.png" width="900px"> </a> </p> <p> This figure from the paper shows a vertical blue highlight for NM_172107.4(KCNQ2):c.635A>G (p.Asp212Gly), the Human Genome Variation Society (HGVS) nomenclature to describe this variant. Located in the KCNQ2 gene, this variant is in a codon for Aspartic acid (D212), and the mutation has been associated with early-onset epileptic encephalopathy, an autosomal dominant inherited disease. The ClinVar Short Variants and SNVs tracks show that all three possible single nucleotide substitutions have been described at this position with pathogenic or likely pathogenic classifications with red blocks (A>C, A>T, A>G). Each described variant leads to a missense change of the Asp residue. The SNV Track Set also includes (discussed in another figure in the paper) computational and predictive components, such as the Rare Exome Variant Ensemble Learner (REVEL) and Combined Annotation Dependent Depletion (CADD) tracks, which calculate impacts of nucleotide changes.</p> <p> The paper also discusses many of the other features developed with the release of Track Sets, @@ -5658,43 +5649,43 @@ hubs employing new extensive <a href="help/trackDb/trackDbHub.html#filter">filter</a> settings available for Track Hubs.</p> <p> The help page is divided into three sections: <ul> <li>filter.fieldName - Used for numerical data</li> <li>filterText.fieldName - Used for text filtering</li> <li>filterValues.fieldName - Used for filtering by pre-specified values or categories in data</li> </ul></p> <p> The <a href="help/hubQuickStartFilter.html#filterText">filterText.fieldName</a> section discusses settings that allow to filter items in a hub with names as seen with this screenshot of only displaying items starting with BRCA using the wildcard match "BRCA*".</p> <p class ="text-center"> <a href="https://genome.ucsc.edu/s/Lou/filterTextExample1"> - <img class="text-center" src="help/examples/hubQuickStartFilter/filterTextExample1.1.png" width="800px"> - <img class="text-center" src="help/examples/hubQuickStartFilter/filterTextExample1.2.png" width="500px"> + <img class="text-center" alt="Text filter configuration example showing filter input fields for track data" src="help/examples/hubQuickStartFilter/filterTextExample1.1.png" width="800px"> + <img class="text-center" alt="Browser results after applying a text filter to narrow displayed track items" src="help/examples/hubQuickStartFilter/filterTextExample1.2.png" width="500px"> </a> </p> <p> The <a href="help/hubQuickStartFilter.html#filterValues">filterValues.fieldName</a> section discusses how to display a drop-down list of options to select items as seen with this screenshot of filtering items that are labeled as either a "DNA-binding region" or "alpha helix" or "beta strand".</p> <p class ="text-center"> <a href="http://genome.ucsc.edu/s/Lou/filterValuesExample2"> - <img class="text-center" src="help/examples/hubQuickStartFilter/filterValuesExample2.1.png" width="800px"> - <img class="text-center" src="help/examples/hubQuickStartFilter/filterValuesExample2.2.png" width="500px"> + <img class="text-center" alt="Value-based filter setup example showing numeric filter range options" src="help/examples/hubQuickStartFilter/filterValuesExample2.1.png" width="800px"> + <img class="text-center" alt="Browser results after applying a value-based filter to track data" src="help/examples/hubQuickStartFilter/filterValuesExample2.2.png" width="500px"> </a> </p> <p> Each section of the <a href="help/hubQuickStartFilter.html">Track Hub Filters Quick Start Guide</a> comes with examples and sessions allowing to quickly click into real interactive demonstration hubs to experiment with how the settings work. The example hubs also provide a starter template for building similar hubs.</p> <p> Many thanks to Lou Nassar for building this Filters Quick Start Guide and Brian Raney for his work implementing the new filter software.</p> <a name="120621"></a> <h2>Dec. 6, 2021 Second of three blog posts about new GenArk hubs</h2> <p> We are pleased to announce the second blog post in a three-part series about @@ -5795,31 +5786,31 @@ tools such as the JSON API, Table Browser, and Data Integrator. We would like to thank the Orphanet team for providing this data. We would also like to thank the UCSC affiliates Chris Lee, Tiana Pereira, and Daniel Schmelter for the creation and release of these tracks. </p> <a name="111721"></a> <h2>Nov. 17, 2021 Releasing A New Genome Browser Track Group: Single-Cell RNA-seq</h2> <p> We are excited to release a new Genome Browser track group with single-cell RNA-seq (scRNA-seq) datasets for the hg38 assembly. Data generated by scRNA-seq allows us to study the heterogeneity of cells in organs, explore gene expression at a cellular level, and track cellular states in both development and disease. <p class ="text-center"> - <img class="text-center" src="../images/newsArchImages/scRNAseq.png" width="70%"></p> + <img class="text-center" alt="Browser display of single-cell RNA-seq expression data tracks" src="../images/newsArchImages/scRNAseq.png" width="70%"></p> <p> We are starting with 14 scRNA-seq tracks covering different major organs of the body. Each new scRNA-seq track contains anywhere from 2-19 individual mRNA expression tracks in <a target="_blank" href="/goldenPath/help/barChart.html">barChart</a> format. By default, tracks display gene expression per individual cell type annotation and are colored according to cell class:</p> <table cellpadding="2"> <thead> <tr> <th style="border-bottom: 2px solid;">Color</th> <th style="border-bottom: 2px solid;">Cell Classification</th> </tr> </thead> <tbody> <tr> @@ -6053,31 +6044,31 @@ per tissue, selected for high-quality and high read depth. The data is summarized to one number per base pair, the number of sequencing reads that cover this position. </li> <li> The plot shows if a given exon is transcribed primarily in certain tissues and whether transcription is uniform over the length of a single exon. </li> <li> Data can also be obtained directly from the <a href="https://gtexportal.org/home/datasets" target="_blank">GTEx Portal</a>. </li> </dd> </dl> <p class ="text-center"> <a href="http://genome.ucsc.edu/s/Lou/GTEx"> - <img class="text-center" src="../images/newsArchImages/GTExV8_eQTL_RNA-seq.jpg" width="800px"> + <img class="text-center" alt="Browser display of GTEx V8 eQTL and RNA-seq tissue expression tracks" src="../images/newsArchImages/GTExV8_eQTL_RNA-seq.jpg" width="800px"> </a> </p> <p> We would like to thank the GTEx investigators, analysts, and portal team for providing this data. We would also like to thank Max Haeussler, Matt Speir, and Jairo Navarro for the creation and release of these tracks. </p> <a name="102121"></a> <h2>Oct. 21, 2021 GENCODE Genes V38 for human (hg38)</h2> <p> We are pleased to announce the release of the <a href="../../cgi-bin/hgTrackUi?db=hg38&c=chrX&g=knownGene">GENCODE Genes V38</a> track for the human (<a href="../../cgi-bin/hgGateway?db=hg38">GRCh38/hg38</a>) Genome Browser.</p> <p> @@ -7460,32 +7451,31 @@ <a name="122320"></a> <h2>Dec. 23, 2020 New ClinVar Interpretations track for human (hg19/hg38)</h2> <p> We are pleased to release a new track, <b>ClinVar Interpretations</b>, for the hg19/GRCh37 and hg38/GRCh38 human assemblies. This track can be found as part of the <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chr10&g=clinvar">ClinVar Composite</a>. It is the first track to use our bead graph display, which is a variation of our existing <a target="_blank" href="#062019">lollipop display</a>.</p> <p> The <b>ClinVar Interpretations track</b> displays the genomic positions of individual variant submissions and interpretations of the clinical significance, as well as their relationship to disease in the ClinVar database. As seen on the image below, the variants are classified into six categories each on a separate horizontal line:</p> <p class="text-center"> - <img class='text-center' src="../images/clinVarInterp.png" width='100%' -alt="ClinVar Interpretations track with bead graph display."> + <img class='text-center' alt="Browser display of ClinVar clinical variant interpretation tracks" src="../images/clinVarInterp.png" width='100%'> </p> <ul> <li><font color="d20000"><b>P</b> - Pathogenic</font></li> <li><font color="d20000"><b>LP</b> - Likely Pathogenic</font></li> <li><font color="000088"><b>VUS</b> - Variant of Unknown Significance</font></li> <li><font color="#00d200"><b>LB</b> - Likely Benign</font></li> <li><font color="#00d200"><b>B</b> - Benign</font></li> <li><font color="#888"><b>OTH</b> - Others</li></font></ul> <p> The size of the bead on the line represents the number of submissions at that genomic position. The color of the beads aids to distinguish the categories further. Hovering on the track items shows the genomic variations which start at that position and the number of individual submissions with that classification. Additional information on the variants @@ -8336,61 +8326,59 @@ Lastly, multiple feature options have been added to both tracks independently:</p> <ul> <li>Filtering by variant length is available on both tracks.</li> <li>Filter by variation (INS, DEL, etc.) now available on both tracks.</li> <li>Filter by clinical significance (benign, conflicting, etc.) now available on both tracks.</li> <li>Filter on allele origin (somatic, germ line, de novo, etc.) now available on both tracks.</li> <li>Filter by molecular consequence (stop lost, nonsense, intron variant, etc.) now available on short variants track.</li> </ul> <p> Below is an example of the filter options available for the <b>ClinVar SNVs track</b>. For additional details on the updated display, see the <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chr1&g=clinvar">track description page</a>.</p> <p class="text-center"> - <img class='text-center' src="../images/clinVarFilters.png" width='60%' -alt="Example of filter options in ClinVar SNVs track"> + <img class='text-center' alt="ClinVar track filter configuration panel for variant pathogenicity" src="../images/clinVarFilters.png" width='60%'> </p> <a name="093020b"></a> <h3>Changes to ClinGen and new tracks</h3> <p> We have created a new composite track, <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chr1&g=clinGenComp">ClinGen</a>, and deprecated the previous <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chr1&g=iscaComposite"> ClinGen CNVs track</a>. The ClinGen CNVs track will continue to be available, however, the data will no longer be updated. This was done by request of ClinGen, as all the data, as well as further updates, can be found in the <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=clinvar">ClinVar Copy Number Variants (ClinVar CNVs) track</a>.</p> <p> The new <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=clinGenComp">ClinGen composite track</a> includes three new tracks described below:</p> <ul> <li><b>ClinGen Dosage Sensitivity Map - Haploinsufficiency</b> - Shows evidence supporting or refuting haploinsufficiency (loss) as mechanisms for disease at gene-level and larger genomic regions.</li> <li><b>ClinGen Dosage Sensitivity Map - Triplosensitivity</b> - Shows evidence supporting or refuting triplosensitivity (gain) as mechanisms for disease at gene-level and larger genomic regions.</li> <li><b>ClinGen Gene-Disease Validity Classification (ClinGen Validity)</b> - Provides a semi-qualitative measurement for the strength of evidence of a gene-disease relationship.</li> </ul> <p class="text-center"> - <img class='text-center' src="../images/clinGenComp.png" width='90%' -alt="Example of three new ClinGen Composite tracks"> + <img class='text-center' alt="Browser display of ClinGen gene-disease clinical validity tracks" src="../images/clinGenComp.png" width='90%'> </p> <p> For more information on these tracks, including display conventions, scores, and classifications, see the <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=clinGenComp">track description page</a>.</p><br> <p> We would like to thank Erin Riggs and May Flowers as well as the rest of the ClinGen team. We would also like to thank ClinVar for making these data available. Track development and release was made possible by Anna Benet-Pages, Christopher Lee, Max Haeussler, and Lou Nassar.</p> <a name="092520"></a> <h2>Sept. 25, 2020   New data and visualization types: Covid GWAS (Lollypop) and Family Trios (VCF Trios)</h2> <h3>Covid GWAS meta-analysis</h3> <p> @@ -9059,31 +9047,31 @@ We are pleased to announce the <em>ENCODE Registry of candidate cis-Regulatory Elements</em> (cCREs) track for the human and mouse genomes (<a href="../../cgi-bin/hgTrackUi?db=hg38&c=chrX&g=encodeCcreCombined" target="_blank">GRCh38/hg38</a> and <a href="../../cgi-bin/hgTrackUi?db=mm10&c=chrX&g=encodeCcreCombined" target="_blank">GRCm38/mm10</a>). cCREs are the subset of representative DNase hypersensitive sites across ENCODE and Roadmap Epigenomics samples that are supported by either histone modifications (H3K4me3 and H3K27ac) or CTCF-binding data. The Registry of cCREs is one of the core components of the integrative level of the <a href="https://www.encodeproject.org/" target="_blank">ENCODE Encyclopedia of DNA Elements</a>. A total of 926,535 elements for human and 339,815 elements for mouse were identified and classified by the ENCODE Data Analysis Center according to biochemical signatures.</p> <a href="http://genome.ucsc.edu/s/Kate/hg38%20ENCODE%20cCRE%20announcement%20largeprint" target="_blank"> -<img style="margin-left" width="950px" src="../images/ccreAnnouncementScreenshot.png"></a> +<img style="margin-left" width="950px" alt="Screenshot of the ENCODE candidate cis-regulatory elements track announcement" src="../images/ccreAnnouncementScreenshot.png"></a> <p> CCREs are colored and labeled according to classification by regulatory signature: <p> <table cellpadding='2'> <tr> <th style="border-bottom: 2px solid;">Color</th> <th style="border-bottom: 2px solid;"></th> <th style="border-bottom: 2px solid;">UCSC label</th> <th style="border-bottom: 2px solid;">ENCODE classification</th> <th style="border-bottom: 2px solid;">ENCODE label</th> </tr> </thead> @@ -9286,31 +9274,31 @@ <p> This track features a horizontal bar chart for each GENCODE gene, resulting in colored bars which show median tissue expression values assayed by the GTEx project in RPKM. Mouse over the bar in the graph shows a tissue specific expression value, while clicking on a chart shows a much larger box-and-whiskers graph for that transcript. The complete tissue color legend and filters are shown on the <a target="_blanK" a href="/cgi-bin/hgGtexTrackSettings?db=hg38&g=gtexGeneV8">GTEx track configuration page</a>. Below the bar graph, a line is shown indicating the gene extent that was used to generate the annotation, colored by gene class using GENCODE conventions (e.g. blue for protein-coding, green for non-coding). </p> <p> <a href = "/cgi-bin/hgGtexTrackSettings?db=hg38&g=gtexGeneV8" target = _blank> -<img src = "../images/GTExV8.png" WIDTH = 750 HEIGHT = 432> +<img alt="GTEx V8 gene expression bar chart track showing expression across tissues" src = "../images/GTExV8.png" WIDTH = 750 HEIGHT = 432> </a> </p> <p> Thank you Kate Rosenbloom and Daniel Schmelter for developing and releasing these tracks</p> <a name="051220"></a> <h2>May 12, 2020 New video: Coronavirus Browser SARS CoV-2 </h2> <p> We are pleased to announce the release of a <a href = "https://www.youtube.com/watch?v=Ee6h0xyZDOM&feature=youtu.be&list=UUQnUJepyNOw0p8s2otX4RYQ" target = _blank>new video</a> on our <a href = "https://www.youtube.com/channel/UCQnUJepyNOw0p8s2otX4RYQ/videos" @@ -9319,31 +9307,31 @@ and molecular biologists developing assays and vaccines. The video highlights many features that regular Browser users may already know, but in the context of SARS-CoV-2 genome assembly. The Browser coronavirus tour highlights RT-PCR data, UniProt , crowd-sourced data, T-cell Reactive epitopes and comparative genomics data for viral isolates from around the world and those infecting other vertebrates. </p> <p> As is our practice, a <a href= "../training/vids/transcript20.pdf" target = _blank>transcript</a> of the voiceover is available. </p> <p> <a href = "https://www.youtube.com/watch?v=Ee6h0xyZDOM&feature=youtu.be&list=UUQnUJepyNOw0p8s2otX4RYQ" target = _blank> - <img src = "../images/titleVid20.jpg" WIDTH = 458 HEIGHT = 258> + <img alt="Thumbnail for the GTEx gene expression tutorial video" src = "../images/titleVid20.jpg" WIDTH = 458 HEIGHT = 258> </a> </p> <p> Thanks to Robert Kuhn for production and Max Haeussler and Jason Fernandes for input. </p> <a name="050620"></a> <h2>May 6, 2020 Problematic Regions for NGS or Sanger sequencing or very variable regions</h2> <p> We are happy to announce a new data track which describes <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg19&g=problematic">Problematic Regions for NGS or Sanger sequencing or very variable regions</a> in the human assembly (hg19/GRCh37).</p> <p> @@ -9640,32 +9628,31 @@ <b>Control Only SV's</b> - gnomAD Structural Variants Controls Only <li> <b>Non-neuro SV's</b> - gnomAD Structural Variants Non-neuro Only </li> </ul> </p> <p> These data can be found as part of the <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg19&g=gnomadSuper">gnomAD</a> super-track. More information on this track can be found in the track description pages, as well as the <a target="_blank" href="https://gnomad.broadinstitute.org/faq">gnomAD</a> site. </p> <p class="text-center"> - <img class='text-center' src="../images/GnomadConstraintStructruralVarRelease.PNG" width='80%' -alt="Example of Constraint Metrics and Structural Variants tracks"> + <img class='text-center' alt="Browser display of gnomAD structural variant constraint scores" src="../images/GnomadConstraintStructruralVarRelease.PNG" width='80%'> </p> <p> We would like to thank the <a target="_blank" href="https://gnomad.broadinstitute.org">Genome Aggregation Database Consortium</a> for making these data available. We would also like to thank Christopher Lee, Maximilian Haeussler, Lou Nassar, Jairo Navarro, Robert Kuhn and Anna Benet-Pages for their effort in the creation of these tracks. </p> <a name="042020"></a> <h2>Apr. 20, 2020 New video on the Browser's YouTube channel</h2> <p> We have released a new video to the Browser's <a href = "https://www.youtube.com/channel/UCQnUJepyNOw0p8s2otX4RYQ/videos" @@ -10099,32 +10086,31 @@ <a href="../../cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite">hg38</a>.</p> <p> We would like to thank NCBI and the RefSeq Annotation database for collecting and curating these data. We would also like to thank Hiram Clawson and Daniel Schmelter for their role creating, documenting, and reviewing these tracks.</p> <a name="020720"></a> <h2>Feb. 7, 2020 New and updated Variants in Papers tracks: Avada variants (hg19) & Mastermind variants (hg19, hg38)</h2> <p> We are pleased to announce a new track, Avada Variants, now available on hg19. Additionally, we have updated the Mastermind Variants track and expanded it to hg38.</p> <p class="text-center"> - <img class='text-center' src="../images/variantsInPapersNewsArch2020.png" width='80%' -alt="Example of AVADA and Mastermind tracks"> + <img class='text-center' alt="Browser display of literature-cited variant annotations from published papers" src="../images/variantsInPapersNewsArch2020.png" width='80%'> </p> <h3>Avada Variants</h3> <p> The Avada Variants track shows the genomic positions of variants in the <a target="_blank" href="http://bejerano.stanford.edu/AVADA/">AVADA database</a>. AVADA is a database of variants built by machine learning software that analyzes full text research articles in PDF format to find genes and variants that look most relevant for genetic diagnosis.</p> <p> Additional information can be found on the <a target="_blank" <a target="_blank" href="https://doi.org/10.1038/s41436-019-0643-6">AVADA publication</a>.</p> <h3>Mastermind Variants</h3> <p> The <a href="#032619">Mastermind Variants</a> track is now available for the hg38 assembly @@ -13626,31 +13612,31 @@ a color-coded checkbox list of the 53 tissues is an interactive illustration of a human anatomical "body map." Hovering over a tissue in the list will highlight the corresponding anatomical region in the body map image. To show or hide tissues in the GTEx Gene Expression track, tissue selections can be made by either selecting tissues in the list or by clicking on the tissue labels in the body map.</p> <p> To quickly see which tissues are selected, right-click the bar graph displayed in the browser for the GTEx track and then click the wrench icon to go to the "Configure GTEx" page. To navigate to the <a href="../cgi-bin/hgGtexTrackSettings?&g=gtexGene" target="_blank">new track settings page</a> from the <a href="../" target="_blank">UCSC Genome Browser</a>, go to the <a href="../cgi-bin/hgGateway?db=hg38" target="_blank">hg38</a> or <a href="../cgi-bin/hgGateway?db=hg19" target="_blank">hg19</a> browser and click on the track label "GTEx" in the Expression group.<br /><br />In the coming months, we plan to incorporate the Tissue Body Map into other GTEx resources.</p> -<!-- <img src="../images/gtexBodyMap.svg" svg width="500" svg height="650"> --> +<!-- <img alt="GTEx body map diagram highlighting tissue-specific gene expression levels" src="../images/gtexBodyMap.svg" svg width="500" svg height="650"> --> <a name="120716"></a> <h2>Dec. 7, 2016 New video: Substitute alternate haplotypes into hg38 chromosome</h2> <p> The Genome Reference Consortium has released many alternate haplotypes as part of the most recent human genome assembly, hg38 (GRCh38). Our new <a href="http://bit.ly/ucscAlts" target="_blank">video tutorial</a>, shows how to use the Genome Browser's multi-region viewing mode to substitute these sequences, along with their annotations, into the main chromosomes of this assembly, as well as other genome assemblies with alternate haplotypes. The video was produced by Robert Kuhn and David Gibson.</p> <p> See our <a href="../training/vids">video page</a> for a full list of our video offerings.</p> <a name="110716"></a> <h2>Nov. 7, 2016 New CRISPR track for many assemblies</h2> @@ -17369,32 +17355,31 @@ modifications suggestive of enhancer and promoter activity, DNAse clusters indicating open chromatin, regions of transcription factor binding, and transcription levels. When viewed in combination, the complementary nature of the data within these tracks has the potential to greatly facilitate our understanding of regulatory DNA.</p> <p> The data comprising these tracks were generated from hundreds of experiments on multiple cell lines conducted by labs participating in the Encyclopedia of DNA Elements (ENCODE) project, and were submitted to the UCSC ENCODE Data Coordination Center for display on the Genome Browser.</p> <p> Faced with the problem of how to display such a large amount of data in a manner facilitating analysis, UCSC has developed new visualization methods that cluster and overlay the data, and then display the resulting tracks on a single screen. Each of the cell lines in a track is associated with a particular color. Light, saturated colors are used to produce the best transparent overlay.</p> <p> -<a href="http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Example1&hgS_otherUserSessionName=hg18EncReg"><img src="/images/encodeRegShot.gif" -alt="ENCODE Regulatory track screenshot" width="622" height="167"></a></p> +<a href="http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Example1&hgS_otherUserSessionName=hg18EncReg"><img alt="ENCODE regulation tracks displayed in the Genome Browser" src="/images/encodeRegShot.gif" width="622" height="167"></a></p> <p> The data in the ENCODE Regulation super-track, as with all data from the production phase of the ENCODE project, have genome-wide coverage. In general, Genome Browser tracks that show ENCODE-generated data can be identified by the double-helix icon preceding the name in the track list. Currently, the ENCODE Regulation data are available only on the Mar. 2006 (NCBI Build 36, UCSC version hg18) assembly of the human genome.</p> <p> For a detailed description of the datasets contained in this super-track and a discussion of how the tracks can be used synergistically to examine regions of regulatory functionality within the genome, see the <a href="../cgi-bin/hgTrackUi?db=hg18&c=chr1&g=wgEncodeReg">track description</a> page.</p> <a name="081810"></a> <h2>Aug. 18, 2010 Cat Genome Browser available</h2> <p> We have released a Genome Browser for the latest assembly of Cat (<em>Felis catus</em>). The GTB @@ -17457,32 +17442,31 @@ We are pleased to announce the release of a new Conservation track based on the zebrafish (danRer6) assembly. This track shows multiple alignments of 6 vertebrate species and measurements of evolutionary conservation using phastCons from the PHAST package. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are displayed in the companion "Most Conserved" track.</p> <p> For more details, please visit the <a href="../cgi-bin/hgTrackUi?db=danRer6&g=multiz6way">track description page</a>.</p> <a name="070710"></a> <h2>Jul. 7, 2010 Happy 10th birthday, Human Genome</h2> <p> <table align=right> <tr> - <td align=right width = 519 height=344><img src = "../../images/10yrGraph4.gif" - alt="10-year usage graph" width="504" height="329"</td> + <td align=right width = 519 height=344><img alt="Graph showing Genome Browser growth in tracks and assemblies over 10 years" src = "../../images/10yrGraph4.gif" width="504" height="329"</td> </tr> <tr> <td align=right><font size=-1>Top graph: total traffic on the UCSC domain during June-July, 2000. Bottom graph: page hit statistics on genome.ucsc.edu in the ensuing years since the Genome Browser was released.<br></font></td> </tr> </table> <p> UCSC is pleased to celebrate the 10-year anniversary of the debut of the first assembled human genome sequence and its then-fledgling visualization tool, the UCSC Genome Browser. Released on July 7, 2000, the genome sequence instantly created unprecedented web traffic on the ucsc.edu domain as researchers around the world scrambled to download the data: 0.5 terabytes per day, a record that stood for many years.</p> <p> David Haussler recounts that day: "Seeing the waterfall of As, Gs, Cs, and Ts pouring off our