Bioperl: Re: Bio::Tools::Blast

[Georg Fuellen]

-re- non-redundant database-builder, Gordon D. Pusch wrote,
> Can anyone suggest a more elegant algorithm than the ``stupid-but-simple''
> method outlined above ???

As a last resort, I would look into suffix trees, which are very
nice for such tasks, and have been used in connection w/ the yeast
database at the MIPS in Munich.

Lincoln wrote, -re- Blast format parsing
> Why don't we come up with a better sequence file standard that
> encapsulates these ideas of identifier, description, source database,
> etc., rather than relying on ad hoc conventions in the FASTA format?

I feel the last thing we need is yet another file format, so I'm 
wondering whether there isn't any good format out there already ?!
For example, we may look into Nexus (which is a pretty generic format), 
or as a last resort maybe even Bio::Seq dumps (via Data::Dumper), 
<other suggestions would be nice>.

> To deal with legacy FASTA files we could have a little reusable
> conversion filter to do the up-front work.
> 
> Lincoln

...
>  > Eitan wrote,
>  > > I would like to warn all Bio::PreSeq::parse_fasta() users. Some fasta 
>  > 
>  > Unless I'm mistaken, there is no reason for any warning, see below.

I've just been talking to Eitan-- his post was based on a misunderstanding
on his side..;-)

best wishes,
Georg Fuellen,
Univ. Bielefeld, Research Group in Practical Comp. Science
http://www.techfak.uni-bielefeld.de/bcd/welcome.html



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