[Bioperl-l] sequence validation

Joel Martin j_martin at mhgc.lbl.gov
Wed Jun 18 14:13:22 EDT 2003

	Voting from the sidelines, I don't expect bioperl or anything
else to validate sequence just because I read it in, if it's suspect
I'd expect to explicitly call the validation routine.  To me it seems
counterintuitive to have to turn that off everytime I read a seq in order
to avoid a performance hit.


On Sat, 14 Jun 2003, William R.Pearson wrote:

> I must point out that, from the point of view of the FASTA program, and
> I think
> BLAST as well, any sequence of printable characters is a "valid" FASTA
> protein
> or DNA sequence.  Letters that do not conform to IUPAC amino-acids or
> nucleotides
> are simply ignored, as are numbers, spaces, tabs, etc.
> Bill Pearson
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

More information about the Bioperl-l mailing list