[Bioperl-l] AlignIO::clustalw bug

[Brian Osborne]

David,

Please file this bug report at http://bugzilla.bioperl.org/, that way we
won't lose track of it.

Thank you,

Brian O.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of David Arenillas
Sent: Wednesday, May 12, 2004 7:23 PM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] AlignIO::clustalw bug

There is a bug in the AlignIO::clustalw::next_aln method whereby it will not
parse files in which the residue number trails the actual nucleotide
sequence. i.e.

CLUSTAL W (1.82) multiple sequence alignment


mm4_dna         ------------------------------------------------------------
hg16_dna        TAAGTCCCCTAAAAGCCATAATTTTTATTATTCCTTTTTCTCTTTTTTCAATTCTATGAA
60


mm4_dna         ------------------------------------------------------------
hg16_dna        TATGTATTATTTTAAAGTTATATTTTTCACACAGAGATGATGCTATATTACACCTTCCCT
120
_______________________________________________
Bioperl-l mailing list
Bioperl-l at portal.open-bio.org
http://portal.open-bio.org/mailman/listinfo/bioperl-l