662f174fa35c933852dabfc4b66654180be3058a jnavarr5 Thu May 13 08:42:32 2021 -0700 Updating HTTP to HTTPS for redirected links, uiLinks cronjob. diff --git src/hg/makeDb/trackDb/spMut.html src/hg/makeDb/trackDb/spMut.html index a085b63..ee1211c6 100644 --- src/hg/makeDb/trackDb/spMut.html +++ src/hg/makeDb/trackDb/spMut.html @@ -1,102 +1,102 @@ <h2>Description</h2> <div class="warn-note" style="border: 2px solid #9e5900; padding: 5px 20px; background-color: #ffe9cc;"> <p><span style="font-weight: bold; color: #c70000;">NOTE:</span><br> This track is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the genome browser database is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions.</p></div> <p> This track shows the genomic positions of natural and artifical amino acid variants in the <a href="https://www.uniprot.org/" target="_blank">UniProt/SwissProt</A> database. The data has been curated from scientific publications by the UniProt staff. </p> <h2>Display Conventions and Configuration</h2> <p> Genomic locations of UniProt/SwissProt variants are labeled with the amino acid change at a given position and, if known, the abbreviated disease name. A "?" is used if there is no disease annotated at this location, but the protein is described as being linked to only a single disease in UniProt. </p> <p> Mouse over a mutation to see the UniProt comments. </p> <p> Artificially-introduced mutations are colored green and naturally-occurring variants are colored red. For full information about a particular variant, click the "UniProt variant" linkout. The "UniProt record" linkout lists all variants of a particular protein sequence. The "Source articles" linkout lists the articles in PubMed that originally described the variant(s) and were used as evidence by the UniProt curators. </p> <h2>Methods</h2> <p> UniProt sequences were aligned to RefSeq sequences first with BLAT, then lifted to genome positions with pslMap. UniProt variants were parsed from the UniProt XML file. The variants 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/" +draws heavily on the <A HREF="https://modbase.compbio.ucsf.edu/LS-SNP/" TARGET="_BLANK">LS-SNP</A> pipeline by Mark Diekhans. The complete script is part of the kent source tree and is located in src/hg/utils/uniprotMutations. </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/$db/bbi/" target="_blank">download server</a>. The underlying data file for this track is called <tt>spMut.bb</tt>. Individual regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt> which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain only features within a given range, for example: <br> <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/uniprot/spMut.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> <h2>Credits</h2> <p> This track was created by Maximilian Haeussler, with advice from Mark Diekhans and Brian Raney. </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>