2593718ac23f10aabf08572b67c20c3db436ef03 max Thu Apr 1 02:09:59 2021 -0700 clarifying the uniprot docs a bit, refs #27308 diff --git src/hg/makeDb/trackDb/uniprot.html src/hg/makeDb/trackDb/uniprot.html index 69006ce..5d47dbf 100644 --- src/hg/makeDb/trackDb/uniprot.html +++ src/hg/makeDb/trackDb/uniprot.html @@ -1,208 +1,216 @@ <h2>Description</h2> <p> -This track shows protein sequence annotations from the <a +This track shows protein sequences and annotations on them from the <a href="https://www.uniprot.org/" target="_blank">UniProt/SwissProt</A> database, -mapped to genomic coordinates. It also shows how the protein sequences in this database -map to the genome. -The data has been curated from scientific publications by the UniProt/SwissProt staff. -The annotations are divided into multiple subtracks, based on their "feature type" in UniProt: +mapped to genomic coordinates. +</p> +<p> +UniProt/SwissProt data has been curated from scientific publications by the UniProt staff, +UniProt/TrEMBL data has been predicted by various computational algorithms. +The annotations are divided into multiple subtracks, based on their "feature type" in UniProt. +The first two subtracks below - one for SwissProt, one for TrEMBL - show the +alignments of protein sequences to the genome, all other tracks below are the protein annotations +mapped through these alignments to the genome. </p> <table class="stdTbl"> <tr> <th>Track Name</th> <th>Description</th> </tr> <tr> - <td>UCSC Alignment, SwissProt</td> + <td>UCSC Alignment, SwissProt = curated protein sequences</td> <td>Protein sequences from SwissProt mapped onto the genome. All other - tracks are (start,end) annotations mapped using this track.</td> </tr> + tracks are (start,end) SwissProt annotations on these sequences mapped + using this track. Protein sequences without a single curated + annotation were not added to this track.</td> </tr> <tr> - <td>UCSC Alignment, TrEMBL</td> + <td>UCSC Alignment, TrEMBL = predicted protein sequences</td> <td>Protein sequences from TrEMBL mapped onto the genome. All other tracks - are (start,end) annotations mapped using this track. This track is -hidden by default. To show it, click its checkbox on the track description -page.</td> </tr> + below are (start,end) TrEMBL annotations mapped to the genome using + this track. This track is hidden by default. To show it, click its + checkbox on the track configuration page. Protein sequences without a single + predicted annotation on them were not added to this track.</td></tr> <tr> <td>UniProt Signal Peptides</td> <td>Regions found in proteins destined to be secreted, generally cleaved from mature protein.</td> </tr> <tr> <td>UniProt Extracellular Domains</td> <td>Protein domains with the comment "Extracellular".</td> </tr> <tr> <td>UniProt Transmembrane Domains</td> <td>Protein domains of the type "Transmembrane".</td> </tr> <tr> <td>UniProt Cytoplasmic Domains</td> <td>Protein domains with the comment "Cytoplasmic".</td> </tr> <tr> <td>UniProt Polypeptide Chains</td> <td>Polypeptide chain in mature protein after post-processing.</td> </tr> <tr> <td>UniProt Regions of Interest</td> <td>Regions that have been experimentally defined, such as the role of a region in mediating protein-protein interactions or some other biological process.</td> </tr> <tr> <td>UniProt Domains</td> <td>Protein domains, zinc finger regions and topological domains.</td> </tr> <tr> <td>UniProt Disulfide Bonds</td> <td>Disulfide bonds.</td> </tr> <tr> <td>UniProt Amino Acid Modifications</td> <td>Glycosylation sites, modified residues and lipid moiety-binding regions.</td> </tr> <tr> <td>UniProt Amino Acid Mutations</td> <td>Mutagenesis sites and sequence variants.</td> </tr> <tr> <td>UniProt Protein Primary/Secondary Structure Annotations</td> <td>Beta strands, helices, coiled-coil regions and turns.</td> </tr> <tr> <td>UniProt Sequence Conflicts</td> <td>Differences between Genbank sequences and the UniProt sequence.</td> </tr> <tr> <td>UniProt Repeats</td> <td>Regions of repeated sequence motifs or repeated domains.</td> </tr> <tr> <td>UniProt Other Annotations</td> <td>All other annotations, e.g. compositional bias</td> </tr> </table> <p> For consistency, the subtrack "UniProt/SwissProt Variants" is a copy of the track "UniProt Variants" in the track group "Phenotype and Literature", or "Variation and Repeats", depending on the assembly. </p> <h2>Display Conventions and Configuration</h2> <p> Genomic locations of UniProt/SwissProt annotations are labeled with a short name for the type of annotation (e.g. "glyco", "disulf bond", "Signal peptide" etc.). A click on them shows the full annotation and provides a link to the UniProt/SwissProt record for more details. TrEMBL annotations are always shown in <span style="color: rgb(0,150,250)"><b>light blue</b></span>, except in the Signal Peptides, Extracellular Domains, Transmembrane Domains, and Cytoplamsic domains subtracks.</p> <p> Mouse over a feature to see the full UniProt annotation comment. For variants, the mouse over will show the full name of the UniProt disease acronym. </p> <p> The subtracks for domains related to subcellular location are sorted from outside to inside of the cell: <span style="color: rgb(255,0,150)"><b>Signal peptide</b></span>, <span style="color: rgb(0,150,255)"><b>extracellular</b></span>, <span style="color: rgb(0,150,0)"> <b>transmembrane</b></span>, and <span style="color: rgb(255,150,0)"><b>cytoplasmic</b></span>. </p> <p> In the "UniProt Modifications" track, lipoification sites are highlighted in <span style="color: rgb(12,12,120)"><b>dark blue</b></span>, glycosylation sites in <span style="color: rgb(0,100,100)"><b>dark green</b></span>, and phosphorylation in <span style="color: rgb(200,200,0)"><b>light green</b></span>.</p> <p> Duplicate annotations are removed as far as possible: if a TrEMBL annotation has the same genome position and same feature type, comment, disease and mutated amino acids as a SwissProt annotation, it is not shown again. Two annotations mapped through different transcripts but with the same genome coordinates are only shown once. </p> <p>Note that only for the human hg38 assembly and SwissProt annotations, there also is a <a href="hgTracks?db=hg38&hubUrl=ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/genome_annotation_tracks/UP000005640_9606_hub/hub.txt">public track hub</a> prepared by UniProt itself, with genome annotations maintained by UniProt using their own mapping method based on those Gencode/Ensembl gene models that are annotated in UniProt for a given protein.</p> <h2>Methods</h2> <p> -UniProt sequences were aligned to UCSC/Gencode transcript sequences first with +UniProt sequences were aligned to one of UCSC, Gencode, Ensembl or Augustus transcript sequences, first with BLAT, filtered with pslReps (93% query coverage, within top 1% score), lifted to genome positions with pslMap and filtered again. UniProt annotations were -obtained from the UniProt XML file. The annotations were then mapped to the +obtained from the UniProt XML file. The UniProt annotations were then mapped to the genome through the alignment using the pslMap program. This mapping approach draws heavily on the <A HREF="http://modbase.compbio.ucsf.edu/LS-SNP/" TARGET="_BLANK">LS-SNP</A> pipeline by Mark Diekhans. For human and mouse, the alignments were filtered by retaining only proteins annotated with a given transcript in the Genome Browser table kgXref. Like all Genome Browser source code, the main script used to build this track can be found on <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/utils/otto/uniprot/doUniprot">github</a>. </p> <h2>Data Access</h2> <p> The raw data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a>, or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/uniprot/" target="_blank">download server</a>. The exact filenames can be found in the <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/trackDb.uniprot.ra">track configuration file</a>. Annotations can be converted to ASCII text by our tool <tt>bigBedToBed</tt> which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain only features within a given range, for example: <br> <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$db/uniprot/unipStruct.bb -chrom=chr6 -start=0 -end=1000000 stdout</tt> <br> This track is updated every month. The MySQL table hgFixed.trackVersion contains the name of the currently available data on the website. Older versions of the data files can be downloaded from the <a href="http://hgdownload.soe.ucsc.edu/goldenPath/$db/archive/">archive folder</a> of our downloads server. <br> Please refer to our <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome">mailing list archives</a> for questions, or our <a href="../FAQ/FAQdownloads.html#download36">Data Access FAQ</a> for more information. </p> <h2>Credits</h2> <p> This track was created by Maximilian Haeussler at UCSC, with help from Chris Lee, Mark Diekhans and Brian Raney, feedback from the UniProt staff and Alejo Mujica, Regeneron Pharmaceuticals. Thanks to UniProt for making all data available for download. </p> <h2>References</h2> <p> UniProt Consortium. <a href="https://academic.oup.com/nar/article/40/D1/D71/2903687/Reorganizing-the-protein-space-at- the-Universal" target="_blank"> Reorganizing the protein space at the Universal Protein Resource (UniProt)</a>. <em>Nucleic Acids Res</em>. 2012 Jan;40(Database issue):D71-5. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22102590" target="_blank">22102590</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245120/" target="_blank">PMC3245120</a> </p> <p> Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E, Bairoch A. <a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.20021" target="_blank"> The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants</a>. <em>Hum Mutat</em>. 2004 May;23(5):464-70. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15108278" target="_blank">15108278</a> </p>