[Bioperl-l] BLAST parameters

[Paul Gordon]

May I suggest that you ask for the top ten hits, rather than use the
default (50?) and parse them out.

> - retrieve the BLAST results and parse out the top ten hits by e-
> value or
> bit-score (undecided if there is a reason to prefer expectation
> values to
> the normalized bit-scores?)
The bit-score will not change over time, but the e-value will depending on
the size of the database.

> Now, my (first) two problems involve submitting the BLAST to NCBI.
> I'm doing a test case with a 3-sequence FASTA file, btw.  What I would
> like is to restrict my BLAST searches to "Rattus norvegicus" as you can on
> the NCBI web-site under advanced options.
Filter the query with a Entrez rat EST query.

blastcl3 -p blastn -W 7 -d est_others -u 'Nucleotide[DB] AND
txid10116[Organism]'

> In addition, I would like to be able to submit customized nucleotide
> substitution matrices to use with the BLAST.

For EST blastns, you might want to use a small word size too (e.g. -W 7).
It might be slower, but there are some things you can do, like use "-S 1"
to search only the forward strand if you have a polyA tail.

Hope that helps,

	Paul

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Paul Gordon
Research Associate
University of Calgary