File Changes for cline

v249_preview to v249_preview2 (2011-03-15 to 2011-03-22) v249

• src/hg/makeDb/doc/uniProt/sp110315.txt
  • lines changed 50, context: html, text, full: html, text
    Downloading a new version of UniProt so we can figure out what's going on with the version number. There's a discrepancy between the current database, sp101005, which gives no version number to the canonical isoform, and the data that's on the web, which gives the canonical isoform a version number of 1. For example, on the web UniProt shows that P46108 has two isoforms, canonical isoform P46108-1 and alternative isoform P46108-2, while sp101005 shows isoforms P46108 and P46108-2. To track this down, markd and I are starting out by loading a fresh copy of UniProt
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 302, context: html, text, full: html, text
    Updating beta
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
  • lines changed 12, context: html, text, full: html, text
    Revised the text of the peptide rank description, based on feedback from Jainab
• src/hg/txCds/txCdsEvFromBed/txCdsEvFromBed.c
  • lines changed 13, context: html, text, full: html, text
    To clear up a problem in the UCSC Genes pipeline, changed the code so that instead of first addressing the longest CDS in each cluster, we address the CDS that has the fewest number of compatible transcripts. In testing against previous output, this cleared up the one strange error condition that was stopping the pipeline. Other than that, it had no effect, aside from changing the order of output slightly for a few lines
• src/hg/txCds/txCdsToGene/txCdsToGene.c
  • lines changed 7, context: html, text, full: html, text
    Changed the code to issue a warning and continue when finding a CDS with a premature stop codon, rather than doing an errAbort. This comes from Rachel and Mark, and their perspective that CCDS contains some transcripts that appear to have PTCs, but don't due to genetic variation. This also follows the growing acceptance that NMD doesn't stop protein translation so much as it turns it down. And the growing acceptance that we don't fully understand NMD.