[Bioperl-l] AlignIO::clustalw bug

David Arenillas dave at cmmt.ubc.ca
Wed May 12 19:23:22 EDT 2004


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


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