[Bioperl-l] Possible bug in Bio::Tools::SeqStats->get_mol_wt?
roy.chaudhuri at gmail.com
Thu Mar 24 09:47:27 EDT 2011
I have discovered a possible bug in Bioperl, although maybe it's my
expectations that are wrong, not the code.
I noticed that when calculating molecular weights for a bunch of protein
sequences using Bio::Tools::SeqStats->get_mol_wt, the values I was
getting were slightly different from the ones given by Emboss pepstats.
This was due to my protein sequences ending with *, since they were
derived from translating annotated genes including the stop codon.
Surprisingly (to me, at least) Bio::Seq->length gives a value that
counts the terminal *, so one greater than the number of amino acids.
SeqStats->get_mol_wt calls Bio::Seq->length to determine the number of
water molecules to subtract from the total molecular weight, so the
reported weights for my sequence were the weight of one water molecule
less than they should have been. I'm not sure if this is a bug in
get_mol_wt, in Bio::Seq->length, or if it's bad practice to use protein
sequences with a terminal asterisk (I've never had a problem doing so
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