[Biojava-l] Blast (bl2seq) parser

[Johan Hattne]

On Thu, 12 Jul 2001, Wiepert, Mathieu wrote:

> So it's the same but with missing sections.  Interesting!  That should
> easily be accommodated codewise then, is it something that people would use,
> or was this a one-off situation for you?

I would expect to use it extensively for our current project. I don't know
about other people, though. Since I have a (ugly) workaround it's not
_really essential_ for me, but I would certainly enjoy a bl2seq parser
along with the others.

// Johan

Lines below included for clarity...

> > Johan,
> >
> > Any chance you want to send me the file you are trying to parse?  I may be
> > able to tell if it is easy to add to the code or not...
>
> I've looked more into it today and found out that the bl2seq output _is_
> just like the blast output with several sections missing, the version
> header being one of them.
>
> What I did to solve the problem was to set up a blast database with just
> one sequence in it and run blast against it to align the second sequence
> to the first. It's not as beautiful a solution as I had hoped but it seems
> to work.
>
> I've attached a sample bl2seq output file. Thank you very much for your
> help!

_______________________________________________________________________________
Johan Hattne * Rackarbergsgatan 34:432 * S-752 32 UPPSALA * SWEDEN * 018-505684
  Mol. Biotech. & Engineering Phys. * auzzie@yodel.net * http://www.yodel.net