[Bioperl-l] build Align object from scratch?

Scott Markel smarkel at scitegic.com
Sat Sep 4 17:24:42 EDT 2004


I did something like this recently.  I used Bio::SimpleAlign,
created Bio::LocatableSeq objects for each member sequence
and added them using $alignment->add_seq().  Worked fine.


Fernan Aguero wrote:
> Hi!
> is it possible to build an alignment object without reading an
> alignment from a file, a filehandle etc?
> I'm reading the pods for AlignIO, AlignI, SimpleAlign, etc
> and I don't see this as a possibility.
> What I'm doing is reading gapped sequences from tables in
> a MySQL database (i.e. already aligned sequences). I need to
> recreate the alignment in my program to then take some
> portions of these sequences based on their overlappings.
> Examples of the kind of sequences that I'll be reading are:
> ATGGTATGGAGTG------------
> --------------TGAGTGTGTGA
> Essentially this looks like an aligned FASTA ... of course I
> could write an alignment in this format to a tmp file and
> then read it again using AlignIO ... but given that I
> already have this info available to my program, I just
> thought this was not the most elegant way to do it.
> Is there another?
> thanks in advance for any tip,
> Fernan

Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at scitegic.com
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