306e80a01217beb1baf7bc65a59cf3c70cabf334 lrnassar Wed Jul 9 18:08:43 2025 -0700 Updating track to reflect that it is now built from GENCODE, not UCSC Genes, refs #25918 diff --git src/hg/makeDb/trackDb/mouse/mm10/gencodePfam.html src/hg/makeDb/trackDb/mouse/mm10/gencodePfam.html new file mode 100644 index 00000000000..ef4906b9de5 --- /dev/null +++ src/hg/makeDb/trackDb/mouse/mm10/gencodePfam.html @@ -0,0 +1,69 @@ +<h2>Description</h2> + +<p> +Most proteins are composed of one or more conserved functional regions called +domains. This track shows the high-quality, manually-curated +<a href="http://pfam.xfam.org" target="_blank"> +Pfam-A</a> +domains found in transcripts located in the GENCODE Genes track by the software HMMER3. +</p> + +<h2>Display Conventions and Configuration</h2> + +<p> +This track follows the display conventions for +<a href="../goldenPath/help/hgTracksHelp.html#GeneDisplay">gene +tracks</a>. +</p> + +<h2>Methods</h2> + +<p> +The sequences from the knownGenePep table (see +<a href="hgTrackUi?g=knownGene">GENCODE Genes description page</a>) +are submitted to the set of Pfam-A HMMs which annotate regions within the +predicted peptide that are recognizable as Pfam protein domains. These regions +are then mapped to the transcripts themselves using the +<a href="http://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank"> +pslMap utility</a>. A complete shell script log for every version of UCSC genes can be found in +our GitHub repository under +<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/ucscGenes/"> +hg/makeDb/doc/ucscGenes</a>, e.g. +<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes17.csh#L1258"> +mm10.knownGenes17.csh</a> is for the database mm10 and version 17 of UCSC known genes. +</p> + +<p> +Of the several options for filtering out false positives, the "Trusted cutoff (TC)" +threshold method is used in this track to determine significance. For more information regarding +thresholds and scores, see the HMMER +<a href="http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf#page=73" +target="_blank">documentation</a> and +<a href="https://hmmer-web-docs.readthedocs.io/en/latest/result.html#profile-hmm-matches" +target="_blank">results interpretation</a> pages. +</p> + +<p> +Note: There is currently an undocumented but known HMMER problem which results in lessened +sensitivity and possible missed searches for some zinc finger domains. Until a fix is released for +HMMER /PFAM thresholds, please also consult the "UniProt Domains" subtrack of the UniProt +track for more comprehensive zinc finger annotations. +</p> + +<h2>Credits</h2> + +<p> +pslMap was written by Mark Diekhans at UCSC. +</p> + +<h2>References</h2> + +<p> +Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, +Forslund K <em>et al</em>. +<a href="https://academic.oup.com/nar/article/38/suppl_1/D211/3112325/The-Pfam-protein-families- +database" target="_blank">The Pfam protein families database</a>. +<em>Nucleic Acids Res</em>. 2010 Jan;38(Database issue):D211-22. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19920124" target="_blank">19920124</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808889/" target="_blank">PMC2808889</a> +</p>