fasta against BLAST2.0 format library

Harry see at sig.for.address
Thu Nov 4 16:43:11 EST 1999

I've been trying to get fasta33t00 to recognize a library/db in BLAST2.0
format (created by NCBI's formatdb, part of the standalone BLAST package).

If I create a fastlib file and point FASTLIB to it, the fasta programs
find and recognize the library fine. However, for my uses, I'd like to run
the fasta programs in a manner that doesn't depend on such a pointer file.
Instead, I'd like to point it at the library file on the command line.

For example:

   fasta33 query.fasta /path/to/blastdb

where the actual library files are blastdb.nsq, .nin, and .nhr.

This generates a "cannot open" error when it gets to the library. This
works fine if the library specified on the command line is in fasta format
so I tried setting LIBTYPE to 12, as described in the docs, to indicate it
is in BLAST2.0 format, but I still get the error.

Is there something I'm missing or is this just not possible and I am
misunderstanding the purpose of LIBTYPE?


Harry <h3 at ucla.edu>

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