0e520097576e90e86ae8b673b660a4dbd436f5b2 max Tue Sep 20 06:36:48 2022 -0700 removing old spUniprot track and moving into eboVir3, the only assembly that now has a track like this, refs #30023 diff --git src/hg/makeDb/trackDb/spUniprot.html src/hg/makeDb/trackDb/spUniprot.html deleted file mode 100644 index d05f51d..0000000 --- src/hg/makeDb/trackDb/spUniprot.html +++ /dev/null @@ -1,104 +0,0 @@ -<h2>Description</h2> - -<p> -This track shows protein sequence annotations from the <a -href="https://www.uniprot.org/" target="_blank">UniProt/SwissProt</A> database, -mapped to genomic coordinates. -The data has been curated from scientific publications by the UniProt staff. -The annotations are divided into two subtracks, one -for all secondary structure annotations and another one for all other -annotations.</p> -<p> -For the mutations curated by UniProt/SwissProt, please open the track -"UniProt Variants" in the track group "Phenotype and Literature". -</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", "disul", "signal pep" etc.). -A click on them shows the full annotation and provides a link to the UniProt/SwissProt -record for more details. </p> - -<p> -Mouse over a feature to see the full UniProt annotation comment. -</p> - -<p> -Modified residues are highlighted in light blue, transmembrane regions in blue, -glycosylation sites in yellow, disulfide bonds in grey, topological domains in -red. -</p> - -<p>Note that for the human hg38 assembly, there also is a -<a href="hgHubConnect">public track hub</a> prepared by UniProt itself, with -genome annotations produced and maintained by UniProt using their mapping -method.</p> - -<h2>Methods</h2> - -<p> -UniProt sequences were aligned to UCSC/Gencode transcript sequences first with -BLAT, then lifted to genome positions with pslMap. UniProt variants were -obtained 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="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/utils/uniprotLift. The exact commands -that were used to build this track can be found on <a -href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/doc/hg38/uniprot.txt">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/$db/bbi/" target="_blank">download server</a>. -The files for this track are called <tt>spAnnot.bb</tt> and <tt>spStruct.bb</tt>. Individual -regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt> -which can be compiled from the source code or downloaded as a precompiled -binary for your system. Instructions for downloading source code and binaries can be found -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. -The tool can also be used to obtain only features within a given range, for example: -<br> -<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/spStruct.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. -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>