NCBI toolkit and binaries

Tom Madden madden at
Wed Sep 22 09:15:27 EST 1999

A new version of the NCBI toolkit source code, as well as binaries for
Sequin, Entrez, blastcl3 and stand-alone BLAST, have been placed on
the NCBI FTP site at

Stand-alone BLAST notes (version 2.0.10):


1.) Bl2seq, a utility to compare two sequences using the blastn or blastp 
is included in the archive.  See the full description in the README.bls for 

2.) A 'sparse' option ('-s') has been added to formatdb.  This option limits the 
for the string identifiers (used by formatdb) to accessions (i.e., no locus 
This is especially useful for sequences sets like the EST's where the accession 
and locus
names are identical.  Formatdb runs faster and produces smaller temporary files 
if this
option is used.  It is strongly recommended for EST's, STS's, GSS's, and HTGS's.

3.) A volume option ('-v') has been added to formatdb.  This option breaks up 
FASTA files into 'volumes' (each with a maximum size of 2 billion letters).
As part of the creation of a volume formatdb writes a new type of BLAST database 
called an alias file, with the extension 'nal' or 'pal', is written.  This 
should be used if one wishes to formatdb large databases (e.g., over 2 billion
base pairs).

4.) It is is now possible to jump start the command line version of PSI-BLAST 
from a multiple alignment that includes the query sequence using the -B option. 
are in README.bls.

5.) The maximum wordsize limit for BLASTN has been removed.

Bug fixes:

1.) A problem if the database length, set by the '-z' option was greater than
2 billion, was fixed.

2.) A core-dump that resulted from the use of the coil-coil masking
('-F C') was fixed by including a file needed for the data directory.

3.) A bug was fixed that caused some very short alignments to be assigned 
expect values.

4.) A bug was fixed that caused formatdb to produce incorrect BLAST databases if
the input was ASN.1.

5.) A serious performance problem with BLASTN and longer words (greater than 16)
was fixed.

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