[EMBOSS] Many-to-many with needle and water

[lueck at ipk-gatersleben.de]

Hi!

I would be interested in "superneedle" if the speed is acceptable. I'm 
still looking for a fast and good enough short sequence finder/aligner 
(see 
http://www.mailinglistarchive.com/biopython@biopython.org/msg00941.html).

At the moment I'm still using BLAST because I have no time to switch 
but later I would like to change to another algorithm.

Kind regards
Stefanie

Zitat von Peter Rice <pmr at ebi.ac.uk>:

> Peter Cock or biopython wrote:
>> Hi Peter R. et al,
>>
>> I gather EMBOSS is looking for feedback for new applications (given
>> the recent funding from the BBSRC - congratulations again). How about
>> suggestions for extensions to existing EMBOSS applications?
>>
>> I've used bits of EMBOSS for several years now (thank you!). Something
>> I have sometimes wanted to do is a many-to-many pairwise sequence
>> alignment with the EMBOSS tools needle and water.
>>
>> Right now, needle and water take two files (here referred to as A and
>> B), file A has just one sequence, and file B can have one or more
>> sequences. I'd like to be able to supply two files both with multiple
>> entries, and have needle/water do pairwise alignments between all the
>> sequences in A against all the sequences in B. This might be useful
>> for finding reciprocal best hits in comparative genomics (as an slower
>> but exact alternative to FASTA or BLAST).
>
> The application is easy to add (after the release)
>
> The usual problem with all-against-all is that it involves loading one
> of the inputs as a sequence set entirely in memory - to avoid reading
> one input many times over.
>
> We have an application supermatcher which does this - the first sequence
> is streamed through, the second is a sequence set loaded into memory. It
> uses work matching to find seed alignments then runs a limited alignment
> around the hits.
>
> superwater would be a possible name (or superneedle).
>
> How popular would such a program be?
>
> How large would the smaller input set be?
>
> regards,
>
> Peter
>
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