Xenopus reference

From Marcotte Lab
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All of these files are derived from XenBase (downloaded on May, 01, 2011).

Version 1. RefSeq of cDNA & protein


  • Used XenBase files: NcbiMrnaXenbaseGene_laevis.txt, xlaevisMRNA.fasta


  • Used XenBase files: NcbiProteinXenbaseGene_laevis.txt, xlaevisProtein.fasta
  1. Read gene name for each NCBI id from 'Ncbi...' file. Filter out genes with 'unnamed' in gene name field.
  2. Read all sequences from '.fasta' file. Convert all sequence character to upper case.
  3. If I find a sequence with '>gi|<gi number>|ref|<genbank accession>' header (means it is RefSeq entity), write it down.