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/gist:167330

Created August 13, 2009 17:37
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gistfile1.txt
my $seqNoGaps = $currentSeq->seq;
$seqNoGaps =~ tr/-//d;
my $domainStartResidue = index($seqNoGaps, $domainSeq)+1;
my $domainEndResidue = $domainStartResidue + length($domainSeq)-1;
my $domainStartColumn = $currentSeq->column_from_residue_number($domainStartResidue);
my $domainEndColumn = $currentSeq->column_from_residue_number($domainEndResidue);
my $alnDomain = $aln->slice($domainStartColumn,$domainEndColumn);
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