We are pleased to announce the DGV Gold Standard track for human (GRCh19/hg19). This track displays copy number variants (CNVs), insertions/deletions (InDels), inversions and inversion breakpoints annotated by the Database of Genomic Variants (DGV). The initial criteria for the Gold Standard set require that a variant be found in at least two different studies and found in at least two different samples. After filtering out low-quality variants, the remaining variants are clustered according to 50% minimum overlap, and then merged into a single record. Gains and losses are merged separately.
-The DGV Gold Standard track +The DGV Gold Standard track utilizes a boxplot-like display to represent the merging of records. The highest ranking variant in the cluster defines the inner "box", while the outer lines define the outermost start and stop coordinates of the CNV. In this way, the inner box forms a high-confidence CNV location and the thin connecting lines indicate confidence intervals for the location of the CNV.
We would like to thank Jeff MacDonald and the Database of Genomic Variants group for providing guidance and these data. We would also like to thank Christopher Lee and Conner Powell as well as the entire UCSC Genome Browser team for creating and releasing this track.
@@ -3022,31 +3022,31 @@We are pleased to announce the release of Allele Specific Expression (ASE) data for the human hg19 and hg38 assemblies. ASE data from the Lappalainen Lab at the New York Genome Center is now available in the UCSC Genome Browser as a public track hub. This track hub contains ASE data identified from transcriptome and genotype data in 53 tissues collected by the Genotype-Tissue Expression (GTEx) project and analyzed by the Lappalainen Lab. The hub contains 3 tracks, a cross tissue summary via density graph of median allelic imbalance, a summary track of all SNPs with evidence of ASE in any tissue, and a composite track showing ASE on a tissue by tissue basis. In the composite track each subtrack is colored based on median ASE for the site across all samples of the tissue, shaded on a spectrum of gray (low) to GTEx convention tissue color (high).
-To access and view this hub, navigate to the Track Hub gateway page and select "GTEx Analysis Hub" from the Public Hubs list. Please direct any queries to Stephane Castel.
Many thanks to Stephane Castel and the Lappalainen Lab at the NY Genome Center for providing this data.
We are pleased to announce the release of four tracks derived from NCBI dbSNP Build 147 data, available on the two most recent human assemblies GRCh37/hg19 and GRCh38/hg38. NCBI's dbSNP database is a collection of "simple nucleotide polymorphisms" (SNPs), which are a class of genetic variations that include single nucleotide polymorphisms and small insertions/deletions (indels). This immense @@ -3130,31 +3130,31 @@
More details about the GENCODE Genes track can be found on the - + GENCODE v24 track description page.
Many thanks to Brian Raney and Luvina Guruvadoo for their work on this track!
We are pleased to announce the release of an updated UCSC Genes track for the Mouse (GRCm38/mm10) assembly. The new release has 63,759 total transcripts, compared with 63,244 in the previous version. The total number of canonical genes has increased from 32,958 to 33,079. Comparing the new gene set with the previous version:
More details about the new GENCODE Basic track can be found on the - + GENCODE Basic track description page.
We are pleased to announce the release of a Genome Browser for the May 2012 assembly of bonobo, Pan paniscus (Max-Planck Institute panpan1, UCSC version panPan1). The assembly was provided by the Max-Planck Institute for Evolutionary Anthropology. There are 10,867 scaffolds with a total size of 2,869,190,071 bases.
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have @@ -4249,42 +4249,42 @@
We are pleased to announce the release of proteomics data for the human hg19 assembly. Data from the National Cancer Institute's (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) is now available in the UCSC Genome Browser as a public track hub. This track hub contains peptides that were identified by CPTAC in their deep mass spectrometry based characterization of the proteome content of breast, colorectal and ovarian cancer biospecimens that were initially sequenced by The Cancer Genome Atlas. This effort extends the accessibility of CPTAC data to more researchers and provides an additional level of analysis to assist the cancer biology community.
-To access and view this hub, navigate to the Track Hub gateway page and select "CPTAC Hub v1" from the Public Hubs list. Please direct any queries to the Fenyo Lab at info@fenyolab.org.
In addition, we have also released a PeptideAtlas track which displays peptide identifications from the PeptideAtlas August 2014 (Build 433) Human build. This build, based on 971 samples containing more than 420 million spectra, identified over a million distinct peptides covering more than 15,000 canonical proteins. To read more about this track, please see the -track description page. Many thanks to Eric Deutsch, Zhi Sun, and the PeptideAtlas team at the Institute for Systems Biology, Seattle for providing this data.
We are pleased to announce the release of a Genome Browser for the June 2014 assembly of cow, Bos taurus (Bos_taurus_UMD 3.1.1, UCSC version bosTau8). This updated cow assembly was provided by the UMD Center for Bioinformatics and Computational Biology (CBCB). This assembly is an update to the previous UMD 3.1 (bosTau6) assembly. UMD 3.1 contained 138 unlocalized contigs that were found to be contaminants. These have been suppressed in UMD 3.1.1.
@@ -4602,31 +4602,31 @@ version on hg19. The total number of canonical genes has increased from 31,848 to 48,424. Comparing the new gene set with the previous version:
More details about the new UCSC Genes track can be found on the -UCSC Genes track description page.
Many thanks to Brian Raney, Jim Kent, and Luvina Guruvadoo for their work on this track.
A Genome Browser is now available for the Chinese hamster (Cricetulus griseus) assembly released July 2013 by the Beijing Genomics Institution-Shenzhen (BGI version C_griseus_v1.0, UCSC version criGri1). For more information and statistics about this assembly, see the NCBI assembly record for C_griseus_v1.0. There are 52,711 scaffolds with a total size of 2,360,146,428 bases.
Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser @@ -4721,43 +4721,43 @@
The Browser's default displayed Transcription Factor ChIP-seq track is updating to the -latest data +latest data release, which has been enhanced with the display of Factorbook motifs. Within a cluster, a green highlight indicates the highest scoring site of a Factorbook-identified canonical motif for the corresponding factor. Upon clicking a transcription factor's cluster with a motif, the details page now displays the motif's sequence logo, alignment and underlying Positional Weight Matrix. Also, the track configuration page now enables the filtering of factors.
The newly added - + Genome Segmentations from ENCODE tracks display multivariate genome-segmentation performed on -six human cell types +six human cell types (GM12878, K562, H1-hESC, HeLa-S3, HepG2, and HUVEC), integrating ChIP-seq data for - + eight chromatin marks, RNA Polymerase II, the CTCF transcription factor and input data. In total, twenty-five states were used to segment the genome, and these states were then grouped and colored to highlight predicted functional elements. These Genome Segmentations are the same data as found in the Analysis Working Group Hub, but are now hosted natively in the Browser with enhanced filtering capability where desired segmented states can be selected using the Filter by Segment Type' control on the track configuration page.
A Genome Browser is now available for the minke whale (Balaenoptera acutorostrata scammoni) assembly released October 2013 by the Korea Ocean Research & Development Institute (KORDI version BalAcu1.0, UCSC version balAcu1). For more information and statistics about this assembly, see the NCBI assembly record for BalAcu1.0. There are @@ -4920,77 +4920,77 @@ cover other costs.
For more information or to submit a request for a workshop, please visit our signup.
We're pleased to announce the release of the Web Sequences track on the UCSC Genome Browser. This track, produced in collaboration with Microsoft Research, contains the results of a 30-day scan for DNA sequences from over 40 billion different webpages. The sequences were then mapped with Blat to the human genome (hg19) and numerous other species including mouse (mm9), rat (rn4), and zebrafish (danRer7). The data were extracted from a variety of sources including patents, online textbooks, help forums, and any other webpages that contain DNA sequence. In essence, this track displays the Blat alignments of nearly every DNA sequence on the internet! The -Web Sequences +Web Sequences track description page contains more details on how the track was generated.
We would like to acknowledge Max Haeussler and Matt Speir from the UCSC Genome Browser staff and Bob Davidson from Microsoft Research for their hard work in creating this track.
We're pleased to add two new assembly hubs produced by the UCSC David Haussler lab to our collection of publicly available hubs. The new hubs feature over 60 bacterial assemblies, including more than 55 different E. coli strains. The assembly annotations include genes, pathogenic genes, conservation, GC percent, repetitive elements and much more.
These hubs focus on comparative genomics and showcase the new "snake" track type. Snakes, which visualize alignments from Hierarchical Alignment (HAL) files, provide a way to view sets of pairwise gapless alignments that may overlap on both the chosen genome (reference) and the query genome, and show various types of genomic variations such as insertions, substitutions, and duplications. More details about the new snake track display and its configuration options can be found on our Genome Browser help page.
To access and view these hubs, navigate to the -Track Hub gateway page +Track Hub gateway page and select one of the two E. coli comparative assembly hubs from the Public Hubs list.
We would like to acknowledge Ngan Nguyen, Glenn Hickey, Brian Raney, Joel Armstrong, Benedict Paten, Matt Speir, and Luvina Guruvadoo for their hard work in creating these hubs.
After 15.4 years of CPU run-time in 9,905,594 individual jobs and 99 cluster runs for lastz pair-wise alignment...we are excited to announce the release of a 100 species alignment on the hg19/GRCh37 human Genome Browser.
This new Conservation track shows multiple alignments of 100 species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package. This adds 40 more species to the existing 60-way on the mm10 mouse browser. For more information about the 100 species Conservation track, see its -description page.
We'd also like to acknowledge the hard work of the UCSC Genome Browser staff who pulled together the information for this track: Hiram Clawson and Pauline Fujita.
The Center for Biomolecular Science and Engineering (CBSE) at UCSC seeks an articulate, self-motivated educator for the two-year position of UCSC Genome Browser trainer. The trainer develops curriculum and provides in-person training on the UCSC Genome Browser at universities, hospitals, institutes, and professional meetings in the United States and internationally. Typical audiences include graduate and post-graduate biologists and doctors, with Genome Browser experience ranging from novice users to bioinformatics specialists. Presentations include formal talks, problem-solving @@ -5225,31 +5225,31 @@
More details about the new UCSC Genes track can be found on the -UCSC Genes track description +UCSC Genes track description page.
Many thanks to Brian Raney, Jim Kent, and Luvina Guruvadoo for their work on this track.
The UCSC Genome Browser is pleased to announce the introduction of a new mirror site to serve our users in Europe. Genome-euro is an official European mirror site of the UCSC Genome Browser at http://genome-euro.ucsc.edu. The server is physically located at the Universität Bielefeld Center for Biotechnology in Bielefeld, Germany, and is administered by UCSC. Genome-euro is meant to be an alternate, faster access point for those Browser users who are geographically closer to central Europe than to the western United States.