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 @@ -31,31 +31,31 @@ <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>