                            Readme for NCBI blast ftp site
                           Last updated on February 15, 2004

    This file lists the subdirectories and files found on the NCBI BLAST
    ftp site (ftp://ftp.ncbi.nlm.nih.gov/blast/).  It provides the basic
    information on file content, and on how the files should be used.

    1. Introduction

    NCBI BLAST ftp site provides standalone blast, client server blast,
    and wwwblast packages for different platforms.  It also provides
    commonly used blast databases in preformatted as well as FASTA format.
    Some documents on the blast executables and other related subjects are
    also provided.

    2. File list and content

    A description of the files are listed in the tables below, one table
    for each directory or subdirectory.

    2.1 ftp://ftp.ncbi.nlm.nih.gov/blast/ directory content

    The blast ftp directory contains several subdirectories each for a
    specific set of files.

    +------------------+-------------------------------------------------+
    |Name              |Content                                          |
    +------------------+-------------------------------------------------+
    blastftp.txt        this file

    db                  subdirectory with database, in preformatted or
                          FASTA form

    demo                demonstration programs and documents from blast
                          developers

    documents           documents for programs in standalone blast,
                          netblast, and wwwblast programs

    executables         archives for binary distribution of blast programs

    matrices            protein and nucleotide score matrices, only a
                          subset are supported by blast

    temp                temporary directory for miscellaneous files
    +------------------+-------------------------------------------------+

    2.2 File content for ftp://ftp.ncbi.nlm.nih.gov/blast/db/ subdirectory

    Databases larger than two gigabytes (2 GB) are formatted in multiple
    volumes, which are named using the “database.##.tar.gz” convention.
    All relevant volumes are required. An alias file is provided so that
    the database can be called using the alias name without the extension
    (.nal or .pal). For example, to call est database, simply use “–d est”
    option in the commandline (without the quotes).

    Certain databases are subsets of a larger parental database. For those
    databases, mask files, rather than actual databases, are provided. The
    mask file needs the parent database to function properly. The parent
    databases should be generated on the same day as the mask file. For
    example, to use swissprot preformatted database, swissprot.tar.gz, one
    will need to get the nr.tar.gz with the same date stamp.

    To use the preformatted blast database file, first inflate the file
    using gzip (unix, linux), WinZip (window), or StuffIt Expander (Mac),
    then extract the component files out from the resulting tar file using
    tar (unix, linux), WinZip (Window), or StuffIt Expander (Mac). The
    resulting files are ready for BLAST.

    +---------------------+----------------------------------------------+
    |Name                 |Content                                       |
    +---------------------+----------------------------------------------+
    FASTA                  subdirectory with databases in FASTA format

    blastdb.txt            content list of the blast database

    est.00.tar.gz          first volume of the est database
    est.01.tar.gz          second volume of the est database
    est.02.tar.gz          third volume of the est database
                           all volumes are needed to reconstitute
                             complete est database

    est_human.tar.gz       human est database, a mask file requires both
                             volumes of est to work

    est_mouse.tar.gz       mouse est database, a maks file needs both
                             volumes of est to work

    est_others.tar.gz      est database without human/mouse entries, a
                             mask file reqires both volumes of est

    gss.tar.gz             genomic survery sequence database

    htgs.00.tar.gz         first volume of the htgs database
    htgs.01.tar.gz         second volume of the htgs database
    htgs.02.tar.gz         all volumes are needed to reconstitute
    htgs.03.tar.gz           complete htgs database

    human_genomic.tar.gz   human chromosome database containing
                             concatenated contigs with adjusted gaps
                             represented by N's

    nr.tar.gz              non-redundant protein database

    nt.00.tar.gz           first volume of the nucleotide nr database
    nt.01.tar.gz           second volume of the nucleotide nr database
    nt.02.tar.gz           all volumes are needed to reconstitute
                             complete nt database

    other_genomic.tar.gz   chromosome database for organisms other than
                             human

    pataa.tar.gz           patent protein database

    patnt.tar.gz           patent nucleotide database

    pdbaa.tar.gz           protein sequence database for pdb entries. It
                             is mask file and requires nr.tar.gz

    pdbnt.tar.gz           nucleotide sequence database for pdb entries.
                             They are not coding sequences for the
                             corresponding protein structure entries!

    sts.tar.gz             sequence tag site database

    swissprot.tar.gz       swissprot sequence database, last major
                             release. It is mask file and requires
                             nr.tar.gz to work properly

    taxdb.tar.gz           taxonomy id database for use with new version
                             of blast database (not fully implemented yet)

    wgs.00.tar.gz          first volume of wgs assembly database
    wgs.01.tar.gz          second volume of the wgs assembly database.
    wgs.02.tar.gz          third volume of the wgs assembly database.
    wgs.03.tar.gz          fourth volume of the wgs assembly database.
    wgs.04.tar.gz          fifth volume of the wgs assembly database.
    wgs.05.tar.gz          sixth volume of the wgs assembly database.
                             all volumes are needed.
    +--------------------+-----------------------------------------------+

    2.2.1 File content for ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA
    subdirectory

    he FASTA database files are now stored in this subdirectory, it does
    contain some additional databases that are not available via the NCBI
    BLAST pages. Due to file size issues, the full est database is not
    provided. One needs to get the three subsets and concatenate them
    together to get the complete est database.

    These databases will need to be formatted using formatdb program found
    in the standalone blast executable package.  The recommended
    commandlines to use are:

            formatdb –i input_db –p F –o T          for nucleotide

            formatdb –i input_db –p T –o T          for protein

    For additional information on formatdb, please see the formatdb.txt
    document under /blast/documents/ directory.

    +------------------+--------------------------------------------------+
    |Name              |Content                                           |
    +------------------+--------------------------------------------------+
     alu.a.gz             proteins translated from alu.n

     alu.n.gz             alu repeat sequences

     drosoph.aa.gz        Drosophila protein from genome annotation

     drosoph.nt.gz        Drosophila genome

     ecoli.aa.gz          E.coli K-12 proteins from genome annotation

     ecoli.nt.gz          E.coli K-12 genomic contigs

     est_human.gz         human subset of the est database

     est_mouse.gz         mouse subset of the est database

     est_others.gz        subset of est other than human or mouse entries

     gss.gz               Genomic Survey Sequences (mostly BAC ends)

     htgs.gz              High Throughput Genomic Sequences

     human_genomic.gz     Human chromosomes formed by concatenating genomic
                            contig assemblies (NT_######) and adjusting the
                            gaps with N’s

     igSeqNt.gz           Immunoglobulin nucleotide sequences

     igSeqProt.gz         Immunoglobulin protein sequences

     mito.aa.gz           protein from the annotated mitochondrial genomes

     mito.nt.gz           mitochondrial genomes
    month.aa.gz
    protein
                            sequences released or updated in the past 30 days

     month.est_human.gz   human subset of EST released/updated in the past
                            30 days

     month.est_mouse.gz   mosue subset of EST released/updated in the past
                            30 days

     month.est_others.gz  EST, wihtout entries from human or mouse, released
                           or updated in the past 30 days

     month.gss.gz         gss entries released/updated in the past 30 days

     month.htgs.gz        htgs entries released/updated in the past 30 days

     month.nt.gz          subset of nt released/updated in the past 30 days

     nr.gz                non-redundant protein sequence database

     nt.gz                nucleotide database from GenBank excluding the
                            batch division htgs, est, gss,sts, pat divisions,
                            and wgs entries.  Not non-redundant.

     other_genomic.gz     Chromosome entries other than human

     pataa.gz             Patent protein sequence database

     patnt.gz             Patent nucleotide sequence database

     pdbaa.gz             protein sequences for pdb entries

     pdbnt.gz             nucleotide entries for pdb entries.  They are NOT
                            the coding sequence forthe corresponding
                            protein entries

     sts.gz               Sequence Tag Sites database

     swissprot.gz         swissprot database, last major release

     vector.gz            vector sequences from synthetic (syn) division
                            of GenBank

     wgs.gz               Whole Genome Shotgun sequence assembly

     yeast.aa.gz          protein translations from yeast genome annotation

     yeast.nt.gz          yeast genomic sequence
    +------------------+----------------------------------------------------+

    2.3 File content for ftp://ftp.ncbi.nlm.nih.gov/blast/demo/ directory

    This directory contains some technical presentations from the BLAST
    developers along with some demo tools or documentation relevant to BLAST.

    +------------------------+-----------------------------------------------+
    |Name                    |Content                                        |
    +------------------------+-----------------------------------------------+
     README.blast_demo         readme for blast_demo package

     README.first              readme for this directory

     README.parse_blast_xml    readme for parse_blast_xml package

     blast_demo.tar.gz         blast_demo package on blast db, blast object,
                                 and reformating blast alignment from
                                 blastobj file

     blast_exercises.doc       blast exercise questions answers

     blast_programming.ppt     PowerPoint presentation on BLAST programing

     blast_talk.ppt            PowerPoint presentation (O'Reilly conference)

     ieee_blast.final.ppt      PowerPoint presentation (IEEE conference)

     ieee_talk.pdf             Above IEEE presentation in PDF format

     parse_blast_xml.tar.gz    demo package on parsing xml styled blast output

     splitd.ppt                PowerPoint presentation on NCBI BLAST server’s
                                 splitd implementation

     test_suite.tar.gz         test package
    +------------------------+-----------------------------------------------+

    2.4 File content for ftp://ftp.ncbi.nlm.nih.gov/blast/documents/ directory

    This directory contains copies of the documentation on different BLAST
    programs distributed from this ftp site under the /blast/executables/
    directory. blast.txt also contains detailed release history.

    +------------------------+-----------------------------------------------+
    |Name                    |Content                                        |
    +------------------------+-----------------------------------------------+
     blast.txt                 readme for blastall and blastpgp

     blastclust.txt            readme for blastclust

     developer                 subdirectory with additional documentation

     blast_seqalign.txt        describing seqalign function

     readdb.txt                describing readdb function

     urlapi.txt                a short introduction on BLAST URL API which
                                 supersedes the blasturl

     formatdb.txt              readme for formatdb program

     impala.txt                readme for impala

     megablast.txt             readme for megablast

     netblast.txt              readme for netblast (blastcl3)

     rpsblast.txt              readme for rpsblast

     xml                       subdirectory with .dtd and .mod field
                                 description files for blast xml output

     xml/NCBI_BlastOutput.dtd  dtd file for blast xml output
     xml/NCBI_BlastOutput.mod  mod file for blast xml output
     xml/NCBI_Entity.mod       mod file for NCBI xml file
     xml/README.blxml          readme on blast xml output
    +------------------------+-----------------------------------------------+

    2.5 File content for ftp://ftp.ncbi.nlm.nih.gov/blast/executables/
    directory

    This directory contains several subdirectories each for a specific
    subsets of executable BLAST programs:

    /LATEST-BLAST subdirectory contains the standalone blast binaries from
            the latest major versioned release.

    /LATEST-NETBLAST sudirectory contains the netblast binaries from the
            latest major versioned release.

    /LATEST-WWWBLAST subdirectory contains the wwwblast binaries from the
            latest major versioned release.

    /release different releases, with the last one linked to LATEST
            directories

    /snapshot subdirectory contains patches or intermediate updates put up in
            between major releases. For previous releases, go to release
            subdirectory, where the old major releases are archived back to
            version 2.0.10.

    2.5.1 File content for ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST-BLAST,
     /LATEST-NETBLAST, and /LATEST-WWWBLAST subdirectories

    All these three subdirectories link to the latest release directory,
    which contains the standalone BLAST executables package (blast initialed
    archives), blastcl3 client (netblast initialed archives), and server blast
    (wwwblast initialed archives).

    The standalone archive is needed to set up BLAST locally on user's own
    machine. It also provides the tools necessary to prepare custom databases
    and retrieve sequences from these prepared databases.  Different archives
    for commonly used platforms are available.

    The blast client archive contains the blastcl3 program which functions by
    formulating BLAST search locally first and forwarding the search to NCBI
    blast server for process. The search results returned by NCBI BLAST server
    is saved to an user-specified file on local computer disk.

    The server blast archive contains the web pages with embedded blast search
    forms similar to that of NCBI that can process the BLAST search request against
    local set of databases and return the result to a browser window. wwwblast
    is now in sync with the NCBI toolkit and the two above two packages.

    +------------------------------------+-------------------------------+
    |Name                                |Content                        |
    +------------------------------------+-------------------------------+
     MD5SUM.txt

     blast-2.2.8-alpha-osf1.tar.gz        Standalone for COMPAQ/HP alpha
                                           machine (OSF 5.1 and above)

     blast-2.2.8-amd64-linux.tar.gz       Standalone for AMD 64-bits PC
                                            running linux

     blast-2.2.8-ia32-freebsd.tar.gz      Standalone for intel Pentium PC
                                            running freeBSD

     blast-2.2.8-ia32-linux.tar.gz        Standalone for intel Pentium PC
                                            running Linux

     blast-2.2.8-ia32-win32.exe           Standalone for intel Pentium PC
                                            running Windows

     blast-2.2.8-ia64-linux.tar.gz        Standalone for intel Itanium PC
                                            running Linux

     blast-2.2.8-mips-irix-32-bit.tar.gz  Standalone for 32-bits SGI

     blast-2.2.8-mips-irix.tar.gz         Standalone for 64-bits SGI

     blast-2.2.8-powerpc-macosx.tar.gz    Standalone for MacOSX (terminal)

     blast-2.2.8-sparc-solaris.tar.gz     Standalone for Sun Sparc station
                                             running Solaris

     netblast-2.2.8-alpha-osf1.tar.gz     netblast for COMPAQ/HP alpha
                                            machine (OSF 5.1 and above)

     netblast-2.2.8-amd64-linux.tar.gz    netblast for AMD 64-bits PC
                                            running Linux

     netblast-2.2.8-ia32-freebsd.tar.gz   netblast for intel Pentium PC
                                            running freeBSD

     netblast-2.2.8-ia32-linux.tar.gz     netblast for intel Pentium PC
                                             running Linux

     netblast-2.2.8-ia32-win32.exe        netblast for for intel Pentium
                                             PC running Windows

     netblast-2.2.8-ia64-linux.tar.gz     netblast for for intel Itanium PC
                                             running Linux

     netblast-2.2.8-mips-irix.tar.gz      netblast for SGI 32-bits system

     netblast-2.2.8-powerpc-macosx.tar.gz netblast for MacOSX

     netblast-2.2.8-sparc-solaris.tar.gz  netblast for Sun Sparc station
                                            running Solaris

     wwwblast-2.2.8-alpha-osf1.tar.gz     wwwblast for COMPAQ/HP alpha
                                            machine (OSF 5.1 and above)

     wwwblast-2.2.8-amd64-linux.tar.gz    wwwblast for AMD 64-bits PC
                                            running Linux

     wwwblast-2.2.8-ia32-freebsd.tar.gz   wwwblast for Intel Pentium PC
                                            running Linux

     wwwblast-2.2.8-ia32-linux.tar.gz     wwwblast for Intel Pentium PC
                                            running Linux

     wwwblast-2.2.8-ia64-linux.tar.gz     wwwblast for Intel Itanium PC
                                            running Linux

     wwwblast-2.2.8-mips-irix.tar.gz      wwwblast for SGI 32-bits system

     wwwblast-2.2.8-powerpc-macosx.tar.gz wwwblast for MacOSX

     wwwblast-2.2.8-sparc-solaris.tar.gz  wwwblast for Sun Sparc station
                                            running Solaris
    +------------------------------------+-------------------------------+

    2.5.2 File content for ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release
    subdirectory

    This directory contains past major releases of BLAST, as far back as
    version 2.0.10. Each release is in its own subdirectory.

    2.5.3 File content for ftp.ncbi.nlm.nih.gov/blast/executables/snapshot
    subdirectory

    This subdirectory contains intermediate enhanced or patched archives
    released after the last major release.  They are organized according
    to the date and only contains the binaries for the affected platforms.

    2.5.4 File content for ftp.ncbi.nlm.nih.gov/blast/executables/special
    subdirectory

    From time to time, we make binaries for some rare platforms under
    special circumstances.  Those files are archived here.

    2.6 File content ftp://ftp.ncbi.nlm.nih.gov/blast/matrices directory

    This directory contains the scoring matrices, which are files that can
    be used by BLAST alignment assessment.  The file are text files with
    special format that can be viewed directly by a browser.

    For valid statistical analysis, blastn uses only identity matrix and
    blastp only supports a limited subset of the BLOSUM and PAM matrices:
    BLOSUM 45, 62, 80, plus PAM30 and 70.

    2.7 File content of the ftp://ftp.ncbi.nlm.nih.gov/blast/temp
    subdirectory

    An left-over subdirectory of miscellaneous files or tools.

    3. Techinical Support

    Additional questions/comments on this ftp site should be directed to
    NCBI blast-help group at:
            blast-help@ncbi.nlm.nih.gov

    Other questions on general NCBI resources should be directed to:
            info@ncbi.nlm.nih.gov