### BLAST-1.2 README file

    September 15, 1991

    Source code for the Basic Local Alignment Search Tool (BLAST) family
    of sequence database comparison programs, along with some support utilities
    and (new) awk scripts, is posted here.  A previous major distribution is
    archived in its entirety beneath the "pub/blast.old" directory.

    Additional source code is necessary to compile and link the BLAST programs:
    the pre-release "ncbi", "gish", and "dfa" libraries.  Source code for these
    libraries is located at the same level in the directory hierarchy as the
    "blast" distribution (currently in /pub/ncbi, /pub/gish, and /pub/dfa).

    The file blast.tar.Z is an L-Z compressed UNIX(R) tar archive containing
    all of the files splayed beneath the "explode" subdirectory.  FTP this
    file to your local machine in binary mode, uncompress it, then untar it.
    The blast.tar file is the same file, just not compressed.  VMS compress
    and tar utilities are posted on this machine in the toolbox/vms_util directory.

    For installation instructions, see the INSTALL file.

    Send bug reports or requests for electronic mail distribution to:

      Dr. Warren Gish, gish@ncbi.nlm.nih.gov
    		or
      Dr. Stephen Altschul, altschul@ncbi.nlm.nih.gov

      National Center for Biotechnology Information
      National Library of Medicine
      Bldg. 38A Rm 8N-806
      8600 Rockville Pike
      Bethesda, MD 20894-0001
      (301) 496-2475

    The people who played a role in bringing this fine software to you:

      Samuel Karlin, Dept. of Mathematics, Stanford Univ., Stanford, CA 94305
      Stephen Altschul, NCBI, NLM, Bethesda, MD 20894
      Webb Miller, Dept. of CS, Penn. State Univ., University Park, PA 16802
      Gene Myers, Dept. of CS, Univ. of Arizona, Tuscon, AZ 85721
      Warren Gish, NCBI, NLM, Bethesda, MD 20894
      David Lipman, NCBI, NLM, Bethesda, MD 20894

    Brief descriptions of the programs:

    blastp:  compare an amino acid query sequence against a protein sequence
    database.

    blastn:  compare a nucleotide query sequence against a nucleotide sequence
    database.

    blastx:  compare a nucleotide query sequence translated in all 6 reading
    frames (3 on each strand) against a protein sequence database.

    tblastn:  compare an amino acid query sequence against a nucleotide sequence
    database translated in all 6 reading frames.

    blast3:  compare an amino acid query sequence against a protein sequence
    database to identify statistically significant 3-way sequence alignments
    (the query sequence plus two database sequences) in which the component
    pairwise alignments are statistically insignificant.

    setdb:  produce a protein sequence database for use by blastp, blastx,
    and blast3 from a multi-sequence file in FASTA format.

    pressdb:  produce a nucleotide sequence database for use by blastn and
    tblastn from a multi-sequence file in FASTA format.

    pam:  generate a PAM matrix of any desired distance (from 2 to 511) and scale.

    pir2fasta:  produce a file in FASTA format from one in NBRF PIR(R) format.

    gb2fasta:  produce a file in FASTA format from one in GenBank(R) format.

    sp2fasta:  produce a file in FASTA format from one in SWISS-PROT(R) format.

    memfile:  manage the loading, updating, and dropping of files mapped into
    shared memory segments.

    Other files:

        blast.1:  UNIX style manual page (using nroff's -man macros) describing
        blastp, blastn, blastx, and tblastn.

        blast.1ps:  PostScript(R) version of blast.1

        blast3.1:  UNIX style manual page describing blast3.

        blast3.1ps:  PostScript version of blast3.1

    	pir2fasta.nawk:  a new awk script for converting NBRF PIR files into FASTA

    	gb2fasta.nawk:  a new awk script for converting GenBank files into FASTA

    	dxch.aa:  a sample protein sequence from the PIR in FASTA format

    Modification history:
        this information has been moved into the file named HISTORY.