fasta-blast replies, thanks

Simon Andrews simon.andrews at
Fri Sep 8 10:43:05 EST 2000

Neil Saunders wrote:

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

I've tried out some of these suggestions, and got a bit stuck here.  I
couldn't find any way to directly reformat the blast output from within
GCG.  The nearest I got was being able to fetch all of the hits, using
the blast output as a list file, and reformat them, but then you get the
entire length, not just the matching fragments.

> (6) Use Fasta-Blast scan from  I
> like this, but I haven't quite figured yet if it gets whole sequences or
> just the portions from the alignment.

This is a lovely little program.  From the short play I had with it, it
appears to use just the fragments, not the entire length which is
retrieved.  It doesn't seem to reference any external database in its
operation, and only the sequence fragments are present in the original
blast/fasta file.

I did find a problem with it though.  When you give it blastp output
from GCG 10.1, the fasta file it writes has no entry after the > on any
file.  This is a problem when performing a bulk reformat, as the
programs die because all sequences have the same name.  This is easy to
fix by hand though.

Thanks for the helpful summary!


Simon Andrews
Molecular Biology Support
BBSRC Bioscience IT Services
e.mail: simon.andrews at
Tel:(+44) 1582 714900
Fax:(+44) 1582 714901

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