[Bioperl-l] Alignment

[Albert Vilella]

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
methods.

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

Cheers,

    Albert.

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
>
> Benachrichtigung bei E-Mail Empfang! - http://mail.lycos.de/app/lycosinside/setupLI.exe
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>