[Bioperl-l] Fwd: problem with bioperl (where's the Mus?)

[Robert Bradbury]

As a really "off-the-wall" suggestion, you might see if somehow the "name"
being pulled is the SwissProt name rather than the species name.  I run into
this when I'm fetching FASTA sequences from SwissProt in that the sequence
identifier names are non-standard for some of the early "standard" species,
e.g.

  "HUMAN",     # Homo sapiens
  "MOUSE",     # Mus musculus
  "RAT",           # Rattus norvegicus
  "BOVIN",       # Bos taurus
  "HORSE",      # Equus caballus
  "PIG",            # Sus scrofa
  "RABIT",        # Oryctolagus cuniculus
  "SHEEP",      # Ovis aries
   "YEAST",     # Saccharomyces cerevisiae (Baker's yeast)
  etc.

Eventually they largely adopted the 3+2 letter species derived name, but the
early "standard" names are anomalies.  You might run a test on a newly
sequenced species (Gorilla, Opossum, Armadillo, Dog, etc.) to see if you get
a "standard" species name.

Robert Bradbury