blastdb_api contains a set of C routines for reading BLAST databases. Version 1.0.3 has just been put on my FTP site.
ftp://saf.bio.caltech.edu/pub/software/molbio/blastdb_api.tar.gz
Changes since 1.02.
A. Fixed the seek by gi function.
B. Added the ability to do gi list based bulk retrieval, equivalent
to the blastall "-l" option.
C. Added the ability to do taxon restricted bulk retrieval
in conjunction with the gi_dbname.bin and gi_dbname.idx files
produced by the gi_subset and prep_taxon_gi files from my
parallelblast distribution. That software may be retrieved
from:
ftp://saf.bio.caltech.edu/pub/software/molbio/parallelblast.tar
the gi_subset and prep_taxon_gi programs may be used separately
from the parallel parts of the code. See the README in that distribution for more information.
A note of caution: NCBI databases often have multiple gi
values associated with a single sequence entry. So in some
cases retrieving by gilist or taxon id (which generates a gilist)
may include the same sequence entry more than once.
Please report any bugs.
Regards,
David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech
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