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

[Peter]

On Mon, Jul 6, 2009 at 10:35 AM, Peter Rice <pmr at ebi.ac.uk> wrote:
>
> 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).

Is see EMBOSS 6.2 has a new tool "needleall" (although if there is a
matching "waterall" the changelog doesn't mention it):
http://lists.open-bio.org/pipermail/emboss/2010-January/003823.html

I'll have to try this out...

Peter