[Bioperl-l] Alignment

marian thieme marian.thieme at lycos.de
Tue Feb 20 08:34:24 EST 2007

Hi all,

perhaps somebody can give some comments in the following matter:

I have a series of sequences which should be aligned against a reference sequence.
In this special case we dont need to calculate anything, we only need to represent the sequences and get for instance some columns of interest.
The problem now is, that some sequences have gaps and we need to represent gaps in the rewference sequence as well as in some individual sequences.

Question: Can I use LocatableSeq to describe sequences with gaps and to add the sequence to the alignment ?
If yes how I have to understand the example in the doc:
use Bio::LocatableSeq;
my $seq = new Bio::LocatableSeq(-seq => "CAGT-GGT",-id  => "seq1", -start => 1,-end   => 7);

Does the "-" sign represents a gap ? When this sequence starts at position 1
why it ends at position 7, because when considering the gap, there are 8 positions.
Does the SimpleAlign object can treat the gap ?

Thanks for your attention,

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