This is to announce that on Sunday, October 30th, the NCBI Experimental BLAST
Network Service will be switched to using the recently announced BLAST version
1.4 sequence database search programs. The version 1.4 programs -- which
include BLASTP, BLASTN, BLASTX, TBLASTN and TBLASTX -- are currently available
for use through the NCBI BLAST E-mail Service and frequently offer better
sensitivity and selectivity than their predecessors. Send a help message to
blast at ncbi.nlm.nih.gov to obtain instructions on the use of the E-mail service.
o The change announced here has to do exclusively with the BLAST Network
Service, as the E-mail Service was converted to using the new programs a few
weeks ago.
o The BLAST3 program is not included in the version 1.4 programs and will not
be affected by this change.
Since the methods used by and format of output from the version 1.4 BLAST
programs is significantly different from that of the old version 1.3 programs,
automated parsers are likely to need modification to maintain correct behavior
upon this change. Compatibility can be checked on real BLAST 1.4 output by
submitting search requests to the NCBI BLAST E-mail Service and attempting to
parse the output returned.
To test parsers on a wider range of problems and output than the NCBI E-mail
Service will allow, the BLAST 1.4 source code is available via anonymous FTP
on ncbi.nlm.nih.gov beneath the /blast directory. Within the blastapp.tar.Z
archive is an Examples subdirectory containing just a few examples of output
from the various programs. Particular attention should be paid to the output
from the new program TBLASTX and to the output from BLASTP when multiple
scoring matrices are used in a single run.
o To test beyond what the E-mail Service and the examples provide, the
UNIX-compatible software will need to be built and tested on a local UNIX
system with local databases.
o The behavior of the old "-gi" command line option to the BLAST programs is
reversed in version 1.4. With the new programs, if NCBI "gi" identifiers are
available for sequences, they will only be displayed if the user specifies the
-gi command line option.
o Under command line control, the BLAST 1.4 programs can optionally produce
ASN.1 structured output that is more accurately parsed than the human-readable
output. Tools to support the ASN.1 output from these programs are under
development, as is a network BLAST server that speaks ASN.1.
Further questions about the BLAST E-mail and Network Services should be
directed to: blast-help at ncbi.nlm.nih.gov
Warren Gish
