8c4eff5f7832be1b022735416a2bb1d4c7ad42be gperez2 Wed Sep 14 13:17:02 2022 -0700 Releasing the UniProt bugs update to the RR, refs #28560 diff --git src/hg/makeDb/trackDb/uniprotAlpha.html src/hg/makeDb/trackDb/uniprotAlpha.html deleted file mode 100644 index 7ca655c..0000000 --- src/hg/makeDb/trackDb/uniprotAlpha.html +++ /dev/null @@ -1,302 +0,0 @@ -<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 to the genome. All other - tracks are (start,end) SwissProt annotations on these sequences mapped - through this alignment. Even protein sequences without a single curated - annotation (splice isoforms) are visible in this track. Each UniProt protein - has one main isoform, which is colored in dark. Alternative isoforms are - sequences that do not have annotations on them and are colored in light-blue. - They can be hidden with the TrEMBL/Isoform filter (see below).</td> </tr> -<tr> - <td>UCSC Alignment, TrEMBL = predicted protein sequences</td> - <td>Protein sequences from TrEMBL mapped to 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. </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 and convenience for users of mutation-related tracks, -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 protein sequence alignments but with the same genome -coordinates are only shown once. </p> - -<p>On the configuration page of this track, you can choose to hide any TrEMBL annotations. -This filter will also hide the UniProt alternative isoform protein sequences because -both types of information are less relevant to most users. Please contact us if you -want more detailed filtering features.</p> - -<p>Note that for the human hg38 assembly and SwissProt annotations, there -also is a <a -href="hgTracks?db=hg38&hubUrl=https://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. For proteins that differ from the genome, UniProt's mapping method -will, in most cases, map a protein and its annotations to an unexpected location -(see below for details on UCSC's mapping method).</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, only for organisms that have a RefSeq transcript track, -proteins are only aligned to the RefSeq transcripts that are annotated -by UniProt for this protein. If no transcripts are annotated on the protein, or -the annotated ones do not exist anymore, but a NCBI Gene ID is annotated, -the RefSeq transcripts for the gene are used. If no NCBI Gene is annotated, -then the best matching alignment is used. Only a handful of edge cases -(pseudogenes, very recently added proteins) on hg38 remain where the -global transcriptome-wide matches have to be used. The details page of the -protein alignments shows the transcripts 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 or several of them do -not differ by more than 1% in alignment score. -</p> - -<p>In other words, when an NCBI or UCSC RefSeq track is used for the mapping and to align a -protein sequence to the correct transcript, we use a three stage process: -<ol> - <li>If UniProt has annotated a given RefSeq transcript for a given protein - sequence, the protein is aligned to this transcript. Any difference in the - version suffix is tolerated in this comparison. - <li>If no transcript is annotated or the transcript cannot be found in the - NCBI/UCSC RefSeq track, the UniProt-annotated NCBI Gene ID is resolved to a - set of NCBI RefSeq transcript IDs via the most current version of NCBI - genes tables. Only the top match of the resulting alignments and all - others within 1% of its score are used for the mapping. - <li>If no transcript can be found after step (2), the protein is aligned to all transcripts, - the top match, and all others within 1% of its score are used. -</ol> - -<p>This system was designed to resolve the problem of incorrect mappings of -proteins, mostly on hg38, due to differences between the SwissProt -sequences and the genome reference sequence, which has changed since the -proteins were defined. The problem is most pronounced for gene families -composed of either very repetitive or very similar proteins. To make sure that -the alignments always go to the best chromosome location, all _alt and _fix -reference patch sequences are ignored for the alignment, so the patches are -entirely free of UniProt annotations. Please contact us if you have feedback on -this process or example edge cases. We are not aware of a way to evaluate the -results completely and in an automated manner.</p> -<p> -Proteins were aligned to transcripts with TBLASTN, converted to PSL, filtered -with pslReps (93% query coverage, keep alignments within top 1% score), lifted to genome -positions with pslMap and filtered again with pslReps. UniProt annotations were -obtained from the UniProt XML file. The UniProt annotations were then mapped to the -genome through the alignment described above using the pslMap program. This approach -draws heavily on the <A HREF="https://modbase.compbio.ucsf.edu/LS-SNP/" -TARGET="_BLANK">LS-SNP</A> pipeline by Mark Diekhans. -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 2-3 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. The exact transcript -that was used for the alignment is shown when clicking a protein alignment -in one of the two alignment tracks. -</p> - -<p> -For reproducibility of older analysis results, 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/$db/uniprot" -target=_blank>downloads server</a>, including the UniProt -protein-to-genome alignment. The file formats available are in the -command line programs liftOver or pslMap, which can be used to map -coordinates on protein sequences to genome coordinates. The filenames are -unipToGenome.over.chain.gz (liftOver) and unipToGenomeLift.psl.gz (pslMap). </p> - -<h2>Data Access</h2> - -<p> -The raw data of the current track can be explored interactively with the -<a href="../cgi-bin/hgTables">Table Browser</a>, or the -<a href="../cgi-bin/hgIntegrator">Data Integrator</a>. -For automated analysis, the genome annotation is stored in a bigBed file that -can be downloaded from the -<a href="http://hgdownload.soe.ucsc.edu/gbdb/$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: -<p> -<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$db/uniprot/unipStruct.bb -chrom=chr6 -start=0 -end=1000000 stdout</tt> -</p> -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 a lot of input 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>