Reformatting of databases for BLAST

Foteos Macrides MACRIDES at WFEB2.BITNET
Fri Oct 4 11:29:00 EST 1991

        Perhaps this question should be posted to bits at ncbi.nlm.nih.gov, but
it relates to recent discussion here about multiply formatted databases, and I
assume those able to answer informatively read both forums.

        Nucleic and protein databases must be reformatted for use with blastn
and blastp, respectively.  What are the considerations and consequences for
maintaining two sets of nucleic and protein blast databases, one set for the
latest quarterly releases, and another set for new sequences that is updated
(reformatted) at daily or weekly intervals?  I suppose what is embedded in
this question is another about the appropriate uses and "abuses" of FastA's
init scores versus blast's probability values w.r.t. the sizes of the
databases searched.

 Foteos Macrides           Worcester Foundation for Experimental Biology
 MACRIDES at WFEB2.BITNET     222 Maple Avenue, Shrewsbury, MA 01545

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