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/uniprot.html src/hg/makeDb/trackDb/uniprot.html index 5d47dbf..d3b8dfd 100644 --- src/hg/makeDb/trackDb/uniprot.html +++ src/hg/makeDb/trackDb/uniprot.html @@ -134,31 +134,31 @@ also is a <a href="hgTracks?db=hg38&hubUrl=ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/genome_annotation_tracks/UP000005640_9606_hub/hub.txt">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.</p> <h2>Methods</h2> <p> UniProt sequences were aligned to one of UCSC, Gencode, Ensembl or Augustus transcript sequences, first with BLAT, filtered with pslReps (93% query coverage, within top 1% score), lifted to genome positions with pslMap and filtered again. UniProt annotations were obtained from the UniProt XML file. The UniProt annotations 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. For human and mouse, the alignments were filtered by retaining only proteins annotated with a given transcript in the Genome Browser table kgXref. 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>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