blast 1.4 "too short" for the size of genbank and embl

Catherine Letondal letondal at pasteur.fr
Tue Aug 4 04:22:05 EST 1998


We maintain a copy of genbank (release + updates) as well as embl for
blast 1.4 searches. The problem is that these databases have reached a 
size that exceeds a 32 bits integer capacity - and this version of blast is
mainly based on such types of integer (more exactly 31 bits, for the
integers are not unsigned). As a result, malloc of negative 
numbers occur.

Of course, we also have the blast 2 NCBI and Washington-Univ. versions.
We are aware that this version of blast is not maintained anymore at NCBI, but
we keep the "old" 1.4 version of blast for compatibility reasons
with blast output parsers (like bob, tbob, blast2html, ...). 

Updating blast 1.4 sources by replacing the 32 bits types by long integers
seem very hazardous ...

Does someone here have the same problem, and some solution ?

Thanks in advance,

Catherine LETONDAL        letondal at pasteur.fr

Tel: +33 (1) 40 61 31 91  Institut Pasteur Service d'Informatique Scientifique
Fax: +33 (1) 40 61 30 80  28 rue du Docteur Roux 75724 Paris CEDEX 15 - FRANCE

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net