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

XENLA_cDNA_ref.v1.fasta (8,879 sequences)

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

XENLA_prot_ref.v1.fasta (8,878 sequences; 'taf5' is not annotated as RefSeq in protein, although its corresponding mRNA sequence is annotated as RefSeq.)

  • 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.