fasta-blast replies, thanks

Neil Saunders neil.saunders at unsw.edu.au
Fri Sep 1 04:58:07 EST 2000


> Maybe you could post a summary of your replies or
> give the details about Friard's fasta-blast scan
> that you mention.  I don't think I was following
> that particular thread and it might take awhile
> to search through the biosci archives and your
> suggestions maybe of interest to the group at large.

Good idea.  This was my problem:  I wanted to extract the top hits from a
BLAST search and obtain the sequences as a FASTA file, so as to do a
multiple alignment including my query sequence.  These were the suggestions.

(1) Use the BLAST service at http://dove.embl-heidelberg.de/Blast2/ which
allows you to select the hits and have them sent as FASTA.

(2) Do BLAST at an SRS6 server, then take the results to ClustalW (I don't
find this one very convenient)

(3) Use MVIEW at http://mathbio.nimr.mrc.ac.uk/~nbrown/MView/.  This one
only uses the alignment fragments from the BLAST, not the whole sequences.

(4) Use Netblast at GCG and reformat the results with tofasta.  I haven't
tried this yet.

(5) Use the BioPerl package and a custom Perl script to get the top
sequences from the server.  Someone actually sent me a script but I'm afraid
I deleted it!  If you know who you are, apologies and I'd appreciate it
again!

(6) Use Fasta-Blast scan from http://annhyb.free.fr/others_programs.html.  I
like this, but I haven't quite figured yet if it gets whole sequences or
just the portions from the alignment.

Neil Saunders

--
School of Microbiology & Immunology,
University of New South Wales,
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Australia

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