September 18, 1991

New versions of the Basic Local Alignment Search Tool (BLAST) family
of programs BLASTP, BLASTN, BLASTX, and BLAST3, along with a new addition
to the family, TBLASTN, are available for anonymous ftp on ncbi.nlm.nih.gov
(IP address 130.14.20.1).  Source code for these and other programs is
posted in the pub/blast, pub/dfa, pub/gish, and pub/ncbi subdirectories.

Features of the distribution include:

o  a new program TBLASTN, that compares an amino acid query sequence against
   a nucleotide sequence database.  By default, the database is dynamically
   translated and searched in all 6 reading frames (3 on each strand), with
   command line options to search just the "top" or just the "bottom" strand
   and to select from one of nine built-in genetic codes.

o  a new utility program named "pam" to generate PAM substitution matrices
   of any desired generation (from PAM 2 to PAM 511) and scale.

o  codons which contain IUPAC ambiguity letters are translated by BLASTX and
   TBLASTN into specific amino acids when such inference is possible.

o  second pass, low stringency (using a lower cutoff score) comparisons
   against a database sequence are performed by BLASTP and TBLASTN when they
   find at least one alignment against a sequence that satisfies the primary
   cutoff score.

o  improved report format, including:  a summary section of one-line
   sequence descriptions of those database sequences whose alignments
   satisfied the cutoff score; and a histogram of maximum alignment
   scores for all sequences in the database.

o  each of the 3 sections of the output report (histogram, one-line summaries,
   and sequence alignments) can be independently turned off or regulated
   by command line options.

o  BLASTDB and BLASTMAT environment variables can be used to point the
   programs to alternate directories for database and substitution
   matrix files.

o  tested compatibility with several UNIX platforms, including: Sun
   Microsystems SunOS 4.1.1, Silicon Graphics IRIX 3.3.2, Next 2.1,
   Apple A/UX 2.0.1, AIX/370 1.2.0; at least partial compatibility
   with Hewlett-Packard HP/UX and Cray Research Unicos.

o  support for multiprocessing on Silicon Graphics (SGI) PowerIRIS computers
   running SGI IRIX System V Release 3.3.2 or later, providing typical
   overall improvement in speed of about 7-fold on machines with 8 processors.

o  a new default word length (W) of 3 in the programs BLASTP, BLASTX, TBLASTN,
   and BLAST3, which reduces memory demands at a modest cost in overall
   execution speed.

o  rather than using fixed constants, the default values for parameters
   T (neighborhood word score threshold) and X (alignment extension drop-off
   score) are calculated dynamically, using ad hoc equations that utilize
   measures of information for each individual database query.

o  the default, calculated value for the neighborhood word score threshold
   T is now lower than in the previous distribution, to obtain high
   sensitivity by default (at the expense of increased execution time).

o  on systems which support it, improved utilities to manage memory-resident
   database files using UNIX System V interprocess communication facilities.