Query Sequence - BLAST

Abhinav Das abhinavd at yahoo.com
Tue Nov 25 20:02:56 EST 2003


Thank you for your answer. Now I've been running some queries from the
genbank directory and each *.ffn file has thousands of short running
queries (each new query starting with a gi followed by a number). As I
am going through the runtime of each of those short queries, I find
that most queries take roughly 30-40 seconds to execute. Why is this
happening? Are these short queries part of a larger query and have
been broken down into smaller pieces that have a short execution time?

 -- Abhinav

Simon Andrews <simon.andrews at bbsrc.ac.uk> wrote in message news:<bo5vmk$dce$1 at south.jnrs.ja.net>...
> Abhinav Das wrote:
> > Hi,
> > 
> > I am doing some performance analysis of BLAST and I am looking for
> > some query sequences. I went through NCBI's FTP site and did not find
> > much except for a small test suite. Could anyone point me to some
> > queries that would take roughly 15-40 minutes on a powerful
> > workstation.
> 
> You were looking in the right place to start with.  NCBI has more 
> sequence data than you can shake a stick at!
> 
> Take a look in:
> 
> ftp://ftp.ncbi.nih.gov/genbank/
> 
> ..and just keep downloading sections until you've got enough data to 
> keep you happy.
> 
> Simon.



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