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/[email protected]/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 <[email protected]>:
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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