8c2f7318d8d821de9b2a25750586a94ab5e8c1bb lrnassar Fri Nov 15 18:50:19 2024 -0800 Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM. diff --git src/hg/makeDb/trackDb/sibGene.html src/hg/makeDb/trackDb/sibGene.html index c02cd82..0b3b4d9 100644 --- src/hg/makeDb/trackDb/sibGene.html +++ src/hg/makeDb/trackDb/sibGene.html @@ -1,73 +1,73 @@ <H2>Description</H2> <P> The SIB Genes track is a transcript-based set of gene predictions based on data from RefSeq and EMBL/GenBank. Genes all have the support of at least one GenBank full length RNA sequence, one RefSeq RNA, or one spliced EST. The track includes both protein-coding and non-coding transcripts. The coding regions are predicted using -<A HREF="http://estscan.sourceforge.net" TARGET="_BLANK">ESTScan</A>.</P> +<A HREF="https://estscan.sourceforge.net/" TARGET="_BLANK">ESTScan</A>.</P> <H2>Display Conventions and Configuration</H2> <P> This track in general follows the display conventions for <A HREF="../goldenPath/help/hgTracksHelp.html#GeneDisplay">gene prediction tracks</A>. The exons for putative non-coding genes and untranslated regions are represented by relatively thin blocks while those for coding open reading frames are thicker.</P> <P> This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the <em>genomic codons</em> option from the <em>Color track by codons</em> pull-down menu. Go to the <A HREF="../goldenPath/help/hgCodonColoring.html">Coloring Gene Predictions and Annotations by Codon</A> page for more information about this feature. </P> <P>Further information on the predicted transcripts can be found on the <A HREF="https://ccg.vital-it.ch/tromer/" TARGET="_BLANK">Transcriptome Web interface</A>.</P> <H2>Methods</H2> <P> The SIB Genes are built using a multi-step pipeline: <OL> <LI>RefSeq and GenBank RNAs and ESTs are aligned to the genome with -<A HREF="http://sibsim4.sourceforge.net" TARGET="_BLANK">SIBsim4</A>, keeping +<A HREF="https://sibsim4.sourceforge.net/" TARGET="_BLANK">SIBsim4</A>, keeping only the best alignments for each RNA. <LI>Alignments are broken up at non-intronic gaps, with small isolated fragments thrown out. <LI>A splicing graph is created for each set of overlapping alignments. This graph has an edge for each exon or intron, and a vertex for each splice site, start, and end. Each RNA that contributes to an edge is kept as evidence for that edge. <LI>The graph is traversed to generate all unique transcripts. The traversal is guided by the initial RNAs to avoid a combinatorial explosion in alternative splicing. <LI>Protein predictions are generated. </OL> <H2>Credits</H2> <P> The SIB Genes track was produced on the <A HREF="https://www.vital-it.ch/" TARGET="_BLANK">Vital-IT</A> high-performance computing platform using a computational pipeline developed by Christian Iseli with help from colleagues at the <A HREF="https://www.ludwigcancerresearch.org/" TARGET="_BLANK">Ludwig Institute for Cancer Research</A> and the <A HREF="https://www.sib.swiss/" TARGET="_BLANK">Swiss Institute of Bioinformatics</A>. It is based on data from NCBI <a href="https://www.ncbi.nlm.nih.gov/refseq/" TARGET="_blank">RefSeq</a> and <a href="https://www.ncbi.nlm.nih.gov/genbank/" target="_blank">GenBank</a>/<a href="https://www.embl.org/" target="_blank">EMBL</a>. Our thanks to the people running these databases and to the scientists worldwide who have made contributions to them.</P> <H2>References</H2> <p> Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. <a href="https://academic.oup.com/nar/article/32/suppl_1/D23/2505202/GenBank-update" target="_blank">GenBank: update</a>. <em>Nucleic Acids Res</em>. 2004 Jan 1;32(Database issue):D23-6. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14681350" target="_blank">14681350</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC308779/" target="_blank">PMC308779</a> </p>