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seeking blast to fasta or similar

Neil Saunders s3003334 at pop3.unsw.edu.au
Thu Aug 17 03:49:38 EST 2000

I'm currently websurfing for an answer to this problem, but perhaps someone
knows a quick answer.  Basically, I'm looking for a quick way to download
sequences obtained from a BLAST search and make a multiple Fasta format file
of those hits plus my query sequence.  Currently, I do my BLAST search, then
click on the accession numbers of the best hits to go to the sequence
database entry.  From there I convert them to Fasta, then copy and paste
into a new file.

A slightly quicker way is to use the 'related sequences' facility from a
search at NCBI and download all hits as Fasta.  But this is still quite
tedious.  What I'd really like is a facility that would parse a BLAST file,
extract the top sequences from the database and give them in Fasta format.
Does anyone know of such a thing?


Neil Saunders

School of Microbiology & Immunology,
University of New South Wales,
Sydney 2052,

Ph: +61 2 9385 2093
Fx: +61 2 9385 1591
email: neil.saunders at unsw.edu.au

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