[Bioperl-l] Packages retrieving online alignment sequences

Gregory Jordan greg at ebi.ac.uk
Sat Aug 7 17:14:58 EDT 2010


Maybe I'm just a bit naive here, but what is the expected difference between
accession and ID and why do we need a separate method for each? Seems to me
that one could just have a single method, get_Aln, which determines under
the hood whether the query string is an accession or ID.

It would be nice if the SimpleAlign object had its Annotation filled with
some extra metadata (such as accession, ID, database version number, URI,
etc.).

One other thing: have you thought about adding an Ensembl adaptor? Or maybe
something similar already exists in BioPerl...?

Sure Ensembl provides their own Perl API, but for someone who doesn't want
to go through the hassle of installing it from CVS (pardon my french, but
wtf!?! Who still uses CVS) and learning a whole new API, it might be
convenient to have a simple BioPerl module for quickly grabbing gene family
alignments from the public Ensembl MySQL databases. I'd be willing to help
write the necessary SQL queries for this.

greg

On 6 August 2010 14:11, Jun Yin <jun.yin at ucd.ie> wrote:

> Hi, Dave,
>
> Thx for reminding me this. I will definitely try it.
>
> Cheers,
> Jun Yin
> Ph.D. student in U.C.D.
>
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
>
>
> -----Original Message-----
> From: Dave Messina [mailto:David.Messina at sbc.su.se]
> Sent: Friday, August 06, 2010 2:07 PM
> To: Jun Yin
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Packages retrieving online alignment sequences
>
> Sounds great, Jun!
>
> Did you happen to test your code on very large alignments? I know there's
> one in Pfam that's something like 100,000 sequences. An rRNA, I believe.
>
>
> Dave
>
>
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