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Looking for a protein containing at least two bromodomains and ubiquitously expressed:

  • Obtaining a list of bromodomain containing proteins:
Roberto Sanchez' bromodomain database is used to obtain SwissProt Accession codes for human proteins containing bromo domains.
  • The list is manually inspected and Genbank and other accession codes converted to SW ACs.
  • The list is submitted to EnsMart to retrieve FASTA sequences for the cDNAs of these genes.
Only 36 genes match the query, when 75 unique SW accession codes where submitted. What happened to the others?
  • Masking the repeats:
~/sys/repeatbeater/RepeatBeater.pl xsact.outfile.sort ~/projects/tubu-bromo/ensembl.fasta 2.15 10 70 1
  • Searching EST human:
on isis: megablast -a 6 -i ensembl.fasta.repeatbeated -D 3 -d est_human -o ensembl-est-2.mbout -E 1e-20
  • Then tiquery to calculate tissue summary:
$TISSUEINFO/bin/tiquery -tiac *.tiac -memory -cancerReport out.cancer -organism 'Homo sapiens' -of  -tissueSummary -isTissueSpecific -mostExpressedIn
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