[Bioperl-l] Bio::Root::Exception when using Bio::Seq

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Mon Jun 19 19:30:19 EDT 2006


> -------------------- WARNING ---------------------
> MSG: seq doesn't validate, mismatch is 1
> MSG: Attempting to set the sequence to [ACTG*] which does not look
> healthy
> NOTE: ACTG* represents a sequence of those 4 characters(a valid DNA
> sequence)
> For some reason it is failing on a particular sequence, which is a valid
> DNA sequence. If anyone has any ideas on why this is I would appreciate
> it.

Usually a '*' indicates a STOP codon in a protein sequence.
I don't think it is valid in a DNA sequence?

So my guess is that BioPerl is auto-detecting it as Protein sequence,
as A,C,T,G are all valid amino acids, and * is a stop codon.

So I think BioPerl is doing the right thing.

If you want to force it, try adding a " -alphabet=>'protein' " parameter to the 
Bio:Seq constructor.

-- 
Torsten Seemann
Victorian Bioinformatics Consortium, Monash University, Australia
http://www.vicbioinformatics.com/


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