Open solution to a problem
In this Nodalpoint wiki page Neil takes a lead to solve a problem posed by Rosie on her blog [http://rrresearch.blogspot.com/2007/07/preparing-to-run-blast-locally.html]. This is a good example of how to share the solution of (?typical may be) bioinformatics problem so that others like me have access to authoritative solutions (typical google searches throw lot of junk and it is a challenge to separate wheat from chaff).
Thanks Neil
clipped from wiki.nodalpoint.org
Rosie has a set of genome sequences from 12 strains of H. influenzae
She wants to search them using a file of 2000 39 bp sequences from H. influenzae Rd
In principle, each of the 2000 queries will have one “best match” per genome, generating 24 000 new 39 bp sequences
She’d like to extract those from the alignment data to use for a new alignment.
Let’s look at (1) BLAST, (2) BLAT, (3) EMBOSS packages and (4) parsing.
