[Bioperl-l] is the Bio::Align::AlignI doc right?

Ben Bimber bimber at wisc.edu
Thu Feb 25 07:35:01 EST 2010

below is a Bio::Align::AlignI example found here:


 Title   : column_from_residue_number
 Usage   : $col = $ali->column_from_residue_number( $seqname, $resnumber)

           This function gives the position in the alignment
           (i.e. column number) of the given residue number in the
           sequence with the given name. For example, for the

             Seq1/91-97 AC..DEF.GH
             Seq2/24-30 ACGG.RTY..
             Seq3/43-51 AC.DDEFGHI

           column_from_residue_number( "Seq1", 94 ) returns 5.
           column_from_residue_number( "Seq2", 25 ) returns 2.
           column_from_residue_number( "Seq3", 50 ) returns 9.

Perhaps I am simply misunderstanding the method, but shouldnt the first
example return 6, not 5?

E is the 94th residue.  It is in the 6th column.  Am I missing something?

More information about the Bioperl-l mailing list