1a36012f9f2eb9d087e503b1fd2c37f3a9adedfd max Fri Nov 26 08:11:01 2021 -0800 A major update for the UniProt otto job, refs #28560 diff --git src/hg/makeDb/trackDb/uniprotAlpha.html src/hg/makeDb/trackDb/uniprotAlpha.html new file mode 100644 index 0000000..6b77f0c --- /dev/null +++ src/hg/makeDb/trackDb/uniprotAlpha.html @@ -0,0 +1,264 @@ +<h2>Description</h2> + +<p> +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. +</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 = curated protein sequences</td> + <td>Protein sequences from SwissProt mapped onto the genome. All other + 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 = predicted protein sequences</td> + <td>Protein sequences from TrEMBL mapped onto the genome. All other tracks + 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" target=_blank>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> +Briefly, UniProt protein sequences were aligned to the transcripts associated +with the protein, the top-scoring alignments were retained, and the result was +projected to the genome through a transcript-to-genome alignment. +Depending on the genome, the transcript-genome alignments was either +provided by the source database (NBCI RefSeq), created at UCSC (UCSC RefSeq) or +derived from the transcripts (Ensembl/Augustus). The transcript set is NCBI +RefSeq for hg38, UCSC RefSeq for hg19 (due to alt/fix haplotype misplacements +in the NCBI RefSeq set on hg19). For other genomes, RefSeq, Ensembl and Augustus +are tried, in this order. The resulting protein-genome alignments of this process +are available in the file formats for liftOver or pslMap from our data archive +(see "Data Access" section below). +</p> + +<p>An important step of the mapping process is filtering the alignment from +protein to transcript. Due to differences between the UniProt proteins and the +transcripts and the genome, the best matching transcript is not always the +correct transcript. Therefore, at least when the transcript model is RefSeq, +proteins are only aligned to the RefSeq transcripts that are annotated by +UniProt for this protein (RefSeq version suffixes are skipped). If no +transcripts are annotated on the protein, or the annotated ones are not current +anymore, but a NCBI Gene ID is annotated, all RefSeq transcripts annotated to +this NCBI Gene ID are used. If no NCBI Gene ID is annotated, then the best +matching alignment is used. On hg38, only a handful of edge cases (pseudogenes, +very recently added proteins) remain where the best matches have to be used. +The details page of the protein alignments shows which transcript were used +for the mapping and how these transcripts were found. There can be multiple +transcripts for one protein, as their coding sequences can be identical. +</p> + +<p> +Proteins were aligned to transcripts with TBLASTN, converted to PSL, 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 UniProt annotations were then mapped to the +genome through the alignment using the pslMap program. This mapping approach +draws heavily on the <A HREF="https://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>Automated data updates and release history</h2> +<p> +This track is automatically updated on an ongoing basis, every 3-6 months. +The current version is always shown on the track details page, it includes the +release of UniProt, the version of the transcript set and a unique MD5 that is +based on the protein sequences, the transcript sequences, the mapping file +between both and the transcript-genome alignment. +</p> + +<p> +Previous versions of this track are available for browsing in the form of the +<a href="hgTracks?db=$db&hubUrl=https://hgdownload.soe.ucsc.edu/goldenPath/archive/$db/uniprot/hub.txt" target=_blank> +UCSC UniProt Archive Track Hub</a>. The underlying data of all releases of this track (past +and current) can be obtained from our +<a href="https://hgdownload.soe.ucsc.edu/goldenPath/archive/$db/uniprot" target=_blank>Downloads Server, in the data archive directory</a>. +The UniProt protein-to-genome alignment is also available from there, in file +formats for our command line programs liftOver or pslMap, which can be used to +map coordinates on protein sequences to genome coordinates. The filenames are +unipToGenome.over.chain.gz and unipToGenomeLift.psl.gz. +</p> + +<h2>Data Access</h2> + +<p> +The raw data of the current track can be explored interactively with the +<a href="../cgi-bin/hgTables">Table Browser</a>, or the +<a href="../cgi-bin/hgIntegrator">Data Integrator</a>. +For automated analysis, the genome annotation is stored in a bigBed file that +can be downloaded from the +<a href="http://hgdownload.soe.ucsc.edu/gbdb/$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/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> +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> + +<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, Alejo +Mujica, Regeneron Pharmaceuticals and Pia Riestra, GeneDx. 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>