blastdb_api updated

David Mathog mathog at caltech.edu
Fri Apr 23 09:21:17 EST 2004


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




More information about the Celegans mailing list