[Bioperl-l] Alignment

Albert Vilella avilella at gmail.com
Tue Feb 20 10:30:17 EST 2007

I think the SimpleAlign object contains a set of sequences, each of
which is a LocatableSeq object.

These LocatableSeq objects will have gaps, represented by '-' or
whatever other symbol is specified (I think there are methods for it),
and then one can use methods like column_from_residue_number to map
the coordinates between the primary sequence and the aligned sequence.
The perldoc for LocatableSeq has some examples on how to use these

[Hopefully I haven't written any lie in this message],



On 2/20/07, marian thieme <marian.thieme at lycos.de> wrote:
> 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,
> Marian
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