    Formatdb README
    ------------------

    Table of Contents

        Introduction

        Command Line Options

        Configuration File

        Formatdb Notes/Troubleshooting

                A The -o option and identifiers
                B "SORTFiles failed" message
                C Formatting large FASTA files
                D Piping a database to formatdb without uncompressing
                E Creating custom databases.
                F General troubleshooting tips.
                G "SeqIdParse Failure" error
                H "FileOpen" error

        Appendix 1: The Files Produced by Formatdb

    Introduction
    ------------
    Formatdb must be used in order to format protein or nucleotide source
    databases before these databases can be searched by blastall, blastpgp
    or MegaBLAST. The source database may be in either FASTA or ASN.1
    format.  Although the FASTA format is most often used as input to
    formatdb, the use of ASN.1 is  advantageous for those who are using
    ASN.1 as the common source for other formats such as the GenBank
    report. Once a source database file has been formatted by formatdb it
    is not needed by BLAST. Please note that formatdb does not create
    non-redundant blast databases.

    If you are having problems formatting a BLAST databases please scroll
    down to the "Formatdb Notes/Troubleshooting" section below. Or contact
    the BLAST Desk at blast-help@ncbi.nlm.nih.gov

    Command Line Options
    --------------------
    A list of the command line options and the current version for formatdb may
    be obtained by executing formatdb without options, as in:

        formatdb -

    The formatdb options are summarized below:

    formatdb 2.2.11   arguments:

      -t  Title for database file [String]  Optional

      -i  Input file(s) for formatting (this parameter must be set) [File In]

      -l  Logfile name: [File Out]  Optional default = formatdb.log

      -p  Type of file
             T - protein
             F - nucleotide [T/F]  Optional
        default = T

      -o  Parse options
             T - True: Parse SeqId and create indexes.
             F - False: Do not parse SeqId. Do not create indexes.
     [T/F]  Optional default = F

        If the "-o" option is TRUE (and the source database is in FASTA
        format), then the database identifiers in the FASTA definition
        line must follow the convention of the FASTA Defline Format.
        Please see section "F Note on creating custom databases"
        below.

      -a  Input file is database in ASN.1 format (otherwise FASTA is expected)
             T - True,
             F - False.
     [T/F]  Optional default = F

      -b  ASN.1 database in binary mode
             T - binary,
             F - text mode.
     [T/F]  Optional default = F

        A source ASN.1 database may be represented in two formats -
        ascii text and binary. The "-b" option, if TRUE, specifies that
        input ASN.1 database is in binary format. The option is ignored
        in case of FASTA input database.

      -e  Input is a Seq-entry [T/F]  Optional default = F

        A source ASN.1 database (either text ascii or binary) may
        contain a Bioseq-set or just one Bioseq. In the latter case the
        "-e" switch should be set to TRUE.

      -n  Base name for BLAST files [String]  Optional

        This options allows one to produce BLAST databases with a
        different name than that of the original FASTA file.  For
        instance, one could have a file named 'ecoli.nuc.txt' and and
        format it as 'ecoli':

            formatdb -i ecoli.nuc.txt -p F -o T -n ecoli

            uncompress -c nr.z | formatdb -i stdin -o T -n nr

        This can be used in situations where the original FASTA file is
        not required other than by formatdb.  This can help in a
        situation where disk-space is tight.

      -v  Database volume size in millions of letters [Integer]  Optional
        default = 0
        range from 0 to <NULL>

        This option breaks up large 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 file, called an  alias file, with the  extension 'nal'
        or 'pal'.

      -s  Create indexes limited only to accessions - sparse [T/F]  Optional
        default = F

        This option limits the indices for the string identifiers (used
        by formatdb)  to accessions (i.e., no locus names).  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.

      -V  Verbose: check for non-unique string ids in the database [T/F]  Optional
        default = F

      -L  Create an alias file with this name
            use the gifile arg (below) if set to calculate db size
            use the BLAST db specified with -i (above) [File Out]  Optional

        This option produces a BLAST database alias file using a specified
        database, but limiting the sequences searched to those in the GI list
        given by the -F argument.  See the section "Note on creating an alias file
        for a GI list" for more information.

      -F  Gifile (file containing list of gi's) [File In]  Optional

        This option can be used to specify the GI list for the alias file
        construction (-L option above) or to produce a binary GI list if
        the -B option (below) is set.

      -B  Binary Gifile produced from the Gifile specified above [File Out]  Optional
        This option specifies the name of a binary GI list file.  This option should
        be used with the -F option.  A text GI list may be specified with the -F
        option and the -B option will produce that GI list in binary format.  The
        binary file is smaller and BLAST does not need to convert it, so it can
        be read faster.

      -T  Taxid file to set the taxonomy ids in ASN.1 deflines [File In]  Optional

        This file specifies a text file containing Seq-id string/numeric taxonomy
        id pairs, separated by a single white space character (or tab), one per
        line. Gi numbers can also be used in place of Seq-id strings. Examples:

        % cat seqid-taxid.txt
        lcl|hmm271 4
        lcl|hmm273 6
        lcl|hmm276 9
        % cat gi-taxid.txt
        129295 9031
        129296 9031
        68738 9031

    Configuration File
    ------------------
    Starting from formatdb version 4, we have added a configuration file to allow
    flexibility in specifying the membership and link bits to set in the ASN.1
    defline structures. This feature is available by recompiling the formatdb
    binary with the following compile time flag: -DSET_ASN1_DEFLINE_BITS.
    The membership bit arrays are used to help distinguish sequences that belong
    to a subset database (e.g.: pdb, swissprot) in a non-redundant database
    (e.g.: nr). The link bit arrays are used to indentify which sequences should
    have a user specified "link out" in the blast (html) report. These features
    are still under development and useful within NCBI only. A sample
    configuration file follows:

    ; .formatdbrc: formatdb configuration file
    ;
    ; This information is needed for the new database format, to set
    ; the links and membership information of the structured deflines.

    ;;;;;;;;;;;;;;;;;;; Memberships section ;;;;;;;;;;;;;;;;;;;;;;
    ; This section determines what the bits mean in the membership bit array.
    ; These must be unique positive integers starting with 1.
    ; When adding a new entry, remember to update the value of TotalNum
    ; This information is used to distinguish database subsets (e.g.: pdb,
    ; swissprot) in non-redundant databases (e.g.: nr).
    [MembershipBitNumbers]
    TotalNum = 3
    1  = swissprot
    2  = pdb
    3  = refseq_protein

    ;;;;;;;;;;;;;;;;;;;;;;;; Links section ;;;;;;;;;;;;;;;;;;;;;;;;;;
    ; This section determines what the bits mean in the links bit array.
    ; These must be unique positive integers starting with 1.
    ; When adding a new entry, remember to update the value of TotalNum and
    ; adding the appropriate file paths for each database in the LinkFiles
    ; section.
    ; This is used for the link out feature of the blast result formatter.
    [LinkBitNumbers]
    TotalNum = 4   ; total number of bits used so far
    1 = LocusLink
    2 = UniGene
    3 = Structure
    4 = Geo

    ; These are the paths to the files containing the
    ; gi's whose links will be modified. The format is
    ; <link_type> = <file_path>
    ; where link_type is one of the types of links defined in the LinkBitNumbers
    ; section.
    [LinkFiles]
    LocusLink = /home/joe/locus_gis.txt
    UniGene   = /dev/null
    Structure = /dev/null
    Geo       = /home/john/geo.txt
    ; EOF

    Formatdb Notes/Troubleshooting:
    -------------------------------

    A.) Note on -o option:

    It is always advantageous to use the '-o' option if the database
    identifiers are in the format specified at
    ftp://ftp.ncbi.nih.gov/blast/db/README.  If the database identifiers
    are in this parseable format,  formatdb produces additional indices
    allowing retrieval from the databases by identifier. The databases on
    the NCBI FTP site contain parseable identifiers. It is sufficient if
    the  first word on the FASTA definition line is a unique identifier
    (e.g.,  ">3091 Alcoho de..."). It is necessary to use parseable
    identifiers for the following  cases:

    1.) ASN.1 is to be produced from blastall or blastpgp, then "-o" must
    be TRUE.

    2.) query-anchored alignments are desired (i.e., the '-m' option with a
    non-zero value is used).

    3.) The gi's are desired as part of the output (i.e., '-I' is used).

    4.) fastacmd will be used to fetch sequences from the database by
    accession or gi.

    See Appendix 1: The Files Produced by Formatdb for more information
    in the -o T option.

    B.) Note on "SORTFiles failed" message:

    Formatdb will use the 'standard' temporary directory to sort the string
    indices on disk. Under UNIX this directory is often /var/tmp and if
    there is not enough space there, then the error message: "ERROR:
    [000.000] SORTFiles failed" will be issued.  This can be avoided by
    setting the TMPDIR environment variable to a partition with more free
    space.  This message may also often be avoided by using the sparse
    option (-s) for formatdb described above.

    C.) Note on formatting large (4 Gig and larger) FASTA files:

    A single BLAST database can contain up to 4 billion letters.  If one
    wishes to formatdb a FASTA file containing more letters than this, several
    databases, each of a maximum size of 4 billion bases, will be produced.
    This will be done automatically if the -v argument is not set.  One may
    also specify a smaller size for the volume databases by using the -v option:

    formatdb -i hugefasta -p F -v 2000000000

    This command line will format the "hugefasta" FASTA file as a number of
    database "volumes," each containing a maximum of two billion base
    pairs, as specified by the "-v" option. Two billion is the current
    limitation on the NCBI toolkit command-line parser. The volumes will
    have names consisting of the root database name, "hugefasta" followed
    by a two-digit volume extension, followed by the usual BLAST database
    extensions. These smaller databases can be searched as if they were a
    single entity using:

    blastall -i infile -d hugefasta -p blastn -o out

    In this case, BLAST recognizes that the database "hugefasta" has been
    partitioned into several volumes because it detects a file with the
    name of the root database followed by an extension of "nal" (for
    protein databases, the extension is "pal"). This file specifies a
    database list to be searched when the root database name is specified
    to BLAST. BLAST sequentially searches each database listed in this
    "nal" file and generates output that is indistinguishable from that of
    a single database search. A sample "nal" file, resulting from
    formatting the datafile "hugefasta" into three volumes, is given below.
    The "DBLIST" line can also be edited to specify additional databases to
    be searched.

    #
    # Alias file created Tue Jan 18 13:12:24 2000
    #
    #
    TITLE hugefasta
    #
    DBLIST hugefasta.00 hugefasta.01 hugefasta.02
    #
    #GILIST
    #
    #OIDLIST
    #

    The "nal" and "pal" files can also be used to simplify searches of
    multiple databases created separately. For instance, a file called
    "multi.nal" containing the following lines could be created from
    scratch using a text editor.

    #
    # Alias file created Tue Jan 18 13:12:24 2000
    #
    #
    TITLE multi
    #
    DBLIST part1 part2 part3
    #
    #GILIST
    #
    #OIDLIST
    #

    The "multi.nal" file would allow the three databases, "part1", "part2",
    and "part3", to be searched by specifying a single database name,
    "multi", on the blastall command line as follows:

    blastall -i infile -d multi -p blastn -o out

    The reason for using database volumes, as opposed to simply making the
    indices in the BLAST databases large enough to handle all conceivable
    databases  with an eight-byte 'integer', is that this would have
    doubled the size of the indices  for all searches no matter how small
    the database.  Hence very large FASTA files  are broken down into a
    couple of databases.

    Formatdb must be able to open files larger than 2 Gig in order to work
    on very large files.  This is not a problem on a 64-bit OS and on
    certain 32-bit OS that allows binaries to be made large-file aware.
    The 32-bit Solaris formatdb binary on the NCBI FTP site is now compiled
    large file aware.

    D.) Note on running formatdb on a database without uncompressing it:

    Under UNIX it is possible to uncompress a database on the fly and pipe
    it to formatdb. This can reduce the disk-space needed for running
    formatdb on a large database.  In addition, some operating systems
    cannot write files larger than 2 Gig to disk.  To circumvent this on
    Unix or Linux systems, use a "pipe" system such as:

    uncompress -c nt.Z|formatdb -i stdin -o T -p T -n "nt" -v 100000000

    In this case, no file is written which is larger than 1 Gig and an
    arbitrarily large database is formatted as a set of 1 Gig volumes.
    Note the use of the '-n' option that specifies the name of the
    resulting BLAST database.  Note also that 'stdin' specifies that input
    will be coming from 'standard input'.  The nt FASTA file is not needed
    for running BLAST searches and nt.Z may be deleted after formatdb has
    been run.

    E) Note on creating custom databases

    With Standalone BLAST it is possible to take any custom file of FASTA
    sequences and use these as a database source file for searching. All
    BLAST database source files must be in FASTA format. In order to use
    the formatdb option -o T, especially for use with NCBI tool kit retrieval
    tools the FASTA defline must follow a specific format.

    F) Note on creating an alias file for a GI list.

    Formatdb can now produce a BLAST database alias file that specifies a (real)
    BLAST database to search as well as a GI list to limit the search.  This
    is useful if one often searches a subset of a database (e.g., based
    on organism or a curated list).  The alias file makes the search appear as
    if one were searching a real database rather than the subset of one.
    The procedure to produce an alias file for searching (protein) nr limiting it to a
    list of zebrafish GI's would be:

    1.) obtain the list of zebrafish GI's from Entrez or some other source and
    keep it in a file called "zebrafish.gi.in".

    2.) invoke formatdb to convert the text GI list to the more efficient binary format:

    formatdb -F zebrafish.gi.in -B zebrafish.gi

    3.) invoke formatdb with the following options:

    formatdb -i nr -p T -L zebrafish -F zebrafish.gi -t "My zebrafish database"

    This will produce the alias file zebrafish.pal listing the database title, the
    real database to be searched, the GI file, and some statistics:

    #
    # Alias file created Thu Jul  5 15:04:29 2001
    #
    #
    TITLE My zebrafish database
    #
    DBLIST nr
    #
    GILIST zebrafish.gi
    #
    #OIDLIST
    #
    NSEQ 1836
    LENGTH 640724

    One can search this by invoking (for example):

    blastall -p blastp -d zebrafish -i MYQUERY -o MYOUTPUT

    NOTE: One may wish to prepare the alias file in one directory, but move it
    to a different production directory that does not contain the real database.
    In that case you may use the '-n' option to specify a path to the real
    database in the production environment.  In the example below the -n option is
    used to specify that the nr database can really be found at a relative path
    of ../../newest_blast/blast

    formatdb -i nr -n ../../newest_blast/blast/nr -p T -L zebrafish -F zebrafish.gi -t "My zebrafish database"

    and the alias file will be:

    #
    # Alias file created Wed Nov 28 13:55:41 2001
    #
    #
    TITLE My zebrafish database
    #
    DBLIST ../../newest_blast/blast/nr
    #
    GILIST zebrafish.gi
    #
    #OIDLIST
    #
    NSEQ 1836
    LENGTH 640724

    Notes on Version 4 of the BLAST databases
    -----------------------------------------

    Version 4 of the BLAST databases address some important
    shortcomings of the current (version 4) databases:

    1.) Version 3 does not handle ambiguity characters correctly if a
    database sequence is longer than about 16 million bases which may
    lead to incorrect results.  The new version does.

    2.) Version 3 only allows one volume of a BLAST database to
    contain at most about 4 billion bases.  The new databases allows that to
    be much larger.

    PLEASE NOTE THAT VERSION 3 OF THE BLAST DATABASES WILL NO LONGER BE SUPPORTED.

    The new databases keep the sequence descriptors in a structured format
    (ASN.1) and some new information has been put into those fields.  The new
    information is:

    1.) taxid.  This integer specifies the taxonomy of the sequence and will
    allow greater flexibility in how taxonomic information is presented in a
    future version of BLAST.

    2.) link bits.  These specify whether LinkOut information about the database
    sequence is available and permits the additon of a gif with a link to the relevant page.
    in a future version of BLAST.

    3.) membership bits.  These specify that a given gi in a database also belongs to
    a subset database.  An example of this relationship is the EST's database.  Est
    contains all EST's, but also comprises est_human, est_mouse and est_others; with
    the new membership bit it will be possible to search any of the subset est databases
    with only the main est database and two other small files (an alias file and an "oidlist").
    This can reduce the amount of disk-space and memory needed by half in this case.
    It is expected that the proper alias file and oidlist for searching such subsets will
    be made available on the NCBI FTP site in mid January.

    FASTA Defline Format
    --------------------
    The syntax of FASTA Deflines used by the NCBI BLAST server depends on
    the database from which each sequence was obtained.  The table below lists
    the identifiers for the databases from which the sequences were derived.

      Database Name                         Identifier Syntax

      GenBank                               gb|accession|locus
      EMBL Data Library                     emb|accession|locus
      DDBJ, DNA Database of Japan           dbj|accession|locus
      NBRF PIR                              pir||entry
      Protein Research Foundation           prf||name
      SWISS-PROT                            sp|accession|entry name
      Brookhaven Protein Data Bank          pdb|entry|chain
      Patents                               pat|country|number
      GenInfo Backbone Id                   bbs|number
      General database identifier           gnl|database|identifier
      NCBI Reference Sequence               ref|accession|locus
      Local Sequence identifier             lcl|identifier

    For example, an identifier might be "gb|M73307|AGMA13GT", where the "gb" tag
    indicates that the identifier refers to a GenBank sequence, "M73307" is its
    GenBank ACCESSION, and "AGMA13GT" is the GenBank LOCUS.

    "gi" identifiers are being assigned by NCBI for all sequences contained
    within NCBI's sequence databases.  The 'gi' identifier provides a uniform
    and stable naming convention whereby a specific sequence is assigned
    its unique gi identifier.  If a nucleotide or protein sequence changes,
    however, a new gi identifier is assigned, even if the accession number
    of the record remains unchanged. Thus gi identifiers provide a mechanism
    for identifying the exact sequence that was used or retrieved in a
    given search.

    For searches of the nr protein database where the sequences are derived
    from conceptual translations of sequences from the nucleotide databases
    the following syntax is used:

                         gi|gi_identifier

    An example would be:

            gi|451623           (U04987) env [Simian immunodeficiency..."

    where '451623' is the gi identifier and the 'U04987' is the accession
    number of the nucleotide sequence from which it was derived.

    Users are encouraged to use the '-I' option for Blast output which will
    produce a header line with the gi identifier concatenated with the database
    identifier of the database from which it was derived, for example, from a
    nucleotide database:

            gi|176485|gb|M73307|AGMA13GT

    And similarly for protein databases:

            gi|129295|sp|P01013|OVAX_CHICK

    The gnl ('general') identifier allows databases not on the above list to
    be identified with the same syntax.  An example here is the PID identifier:

            gnl|PID|e1632

    PID stands for Protein-ID; the "e" (in e1632) indicates that this ID
    was issued by EMBL.  As mentioned above, use of the "-I" option
    produces the NCBI gi (in addition to the PID) which users can also
    retrieve on.

    The bar ("|") separates different fields as listed in the above table.
    In some cases a field is left empty, even though the original
    specification called for including this field.  To make
    these identifiers backwards-compatiable for older parsers
    the empty field is denoted by an additional bar ("||").

    BLAST Databases without GI's or GenBank accessions
    --------------------------------------------------
    Some BLAST users wish to format a FASTA file of sequences that do not
    contain NCBI ID's such as accessions or GI numbers.  This may be the
    case if the sequences have not yet been submitted to GenBank or are
    proprietary.  If the only goal is to perform BLAST searches and format
    a standard BLAST report then the simplest solution is to not set the
    "-o" option when running formatdb and indices for the identifiers will
    not be constructed.  If one wishes to produce XML or ASN.1 output or
    wants to fetch sequences by ID with fastacmd, it is necessary to
    observe a few simple rules when constructing the ID's.  These rules are
    necessary to ensure that the ID's can be reliably parsed to make the ID
    indices.

    1.) ID's of type "local" or "general" should be used.  This means that
    the ID's will have the syntax "lcl|IDENTIFIER" (for "local") or
    "gnl|DATABASE|IDENTIFIER" (for "general").  The tokens DATABASE and
    IDENTIFIER should be assigned by the user here.  The local ID has only
    one user provided token, the general ID requires two.  The fields are
    separated by vertical bars ("|")..

    2.) Letters, numbers, underscores ("_"), dashes, and periods may be
    used.  Uppercase and lowercase letters are treated as being distinct.
    No spaces are allowed in the ID, this indicates the end of the ID.

    3.) All ID's should be unique, if the entire ID is examined.  As an
    example consider the following four ID's:

    gnl|H.sapiens|seq1
    gnl|H.sapiens|seq2
    gnl|M.Mus|seq1
    lcl|seq1

    All of these ID's are considered unique.  The first two might be
    sequences one and two of a collection of Human sequences; the fourth
    might be the first sequence in a collection of mouse sequences; the
    fourth is simply identified as the first sequence.

    ID's must fit into the framework described above to ensure that they
    can be reliably parsed and indices built for them.  This means that it
    is not possible for users to invent new ID formats on the fly.
    Examples of illegal ID's would be:

    H.sapiens|seq1
    gnl|H.sapiens|seq1|A

    The first identifier is missing a database tag (e.g., no "lcl"), the second
    identifier has an extra field since vertical bars separate fields.  Illegal
    ID's will not be processed by formatdb if the "-o" option is used.

    F. General troubleshooting tips.

    The Latest Version: Make sure you are using the latest version of the
    formatdb executable. Earlier versions of formatdb may not recognize
    changes in the ASN.1 or FASTA definition line format of current BLAST
    databases or other sources of NCBI sequences.

    G. Troubleshooting "SeqIdParse Failure" errors

    The most frequent cause of SeqIdParse Failure errors come from the
    syntax of the FASTA definition lines in the source database file. Many
    third parties do not follow the syntax in section F. If you are
    getting a SeqIdParse error this can often be eliminated by formatting
    the database with the -o option set to FALSE (e.g. -o F). The -o option
    is really not important for BLAST searching unless you are going to use
    the results to parse out the identifiers for searching Entrez and
    downloading the sequences. If you need to use the -o T option then your
    best option is to examine the definition lines of the database sequences
    and attempt to make them conform the FASTA syntax.

    H. Troubleshooting "FileOpen" errors.

    This is caused when the formatdb program can not find the /data
    subdirectory. When you download and extract the Standalone BLAST
    executables, the formatdb program is located in the same directory as
    the /data subdirectory. If either if these move, formatdb will not
    function without a .ncbirc file telling it where the /data subdirectory
    resides. Create a text file in the same directory as formatdb that
    contains the following lines:

    [NCBI]
    Data="path/data/"

    Where "path/data/" is the path to the location of the Standalone BLAST
    "data" subdirectory. For Example:

    Data=/root/blast/data

    For PC's this would be

    [NCBI]
    Data="C:\path\data\"

    Where "C:path\data\" is the path to the location of the Standalone
    BLAST "data" subdirectory. For example:

    Data=C:\blast\data

    For Macintosh this would be a simpletext file called "ncbi.cnf", placed in
    System folder, that contains:

    [BLAST]
    BLASTDB=root:blast:data

    Where "root:blast:data" is the path to the location of the Standalone
    BLAST "data" subdirectory. For example on the machine names "LabMac":

    BLASTDB=LabMac:blast:data

    Appendix 1: The Files Produced by Formatdb
    ------------------------------------------
    Using formatdb without the "-o T" indexing option results in three
    BLAST database files (.nhr, .nin, ,nsq).  Using the "-o T" option will result
    in additional files.
    If gi's are present in the FASTA definition lines of the source file, there
    will be four additional files created (.nsd, nsi, nni, nnd). These are
    ISAM indices for mapping a sequence identifier to a particular sequence in
    the BLAST database. If gi's are not use there will be only two additional
    files created (.nsd, .nsi).
    These files are listed below for both an example nucleotide and a protein
    sequence database. The actual sequence data is stored in the files with
    extension "nsq" or "psq".  The compression ratio for these files is
    about 4:1 for nucleotides and 1:1 for protein sequence source files.

    Extension    Content        Format
    ---------------------------------------------
    Nucleotide database formatted without "-o T"

    nhr          deflines       binary

    nin          indices        binary

    nsq        sequence data    binary

    Nucleotide database formatted with "-o T" add these ISAM files:

    nnd          GI data        binary

    nni          GI indices     binary

    nsd          non-GI data    binary

    nsi         non-GI indices  binary

    The formatdb index files involving deflines are small relative to the
    source database due to entries such as the one below in which the
    defline is much shorter than the sequence.

    >gi|5819095|ref|NC_001321.1| Balaenoptera physalus mitochondrion, complete genome
    GTTAATTACTAATCAGCCCATGATCATAACATAACTGAGGTTTCATACATTTGGTATTTTTTTATTTTTTTTGGGGGGCT
    TGCACGGACTCCCCTATGACCCTAAAGGGTCTCGTCGCAGTCAGATAAATTGTAGCTGGGCCTGGATGTATTTGTTATTT
    GACTAGCACAACCAACATGTGCAGTTAAATTAATGGTTACAGGACATAGTACTCCACTATTCCCCCCGGGCTCAAAAAAC
    TGTATGTCTTAGAGGACCAAACCCCCCTCCTTCCATACAATACTAACCCTCTGCTTAGATATTCACCACCCCCCTAGACA
    GGCTCGTCCCTAGATTTAAAAGCCATTTTATTTATAAATCAATACTAAATCTGACACAAGCCCAATAATGAAAATACATG
    AACGCCATCCCTATCCAATACGTTGATGTAGCTTAAACACTTACAAAGCAAGACACTGAAAATGTCTAGATGGGTCTAGC
    CAACCCCATTGACATTAAAGGTTTGGTCCCAGCCTTTCTATTAGTTCTTAACAGACTTACACATGCAAGTATCCACATCC
    CAGTGAGAACGCCCTCTAAATCATAAAGATTAAAAGGAGCGGGTATCAAGCACGCTAGCACTAGCAGCTCACAACGCCTC
    GCTTAGCCACGCCCCCACGGGACACAGCAGTGATAAAAATTAAGCTATAAACGAAAGTTCGACTAAGTCATGTTAATTTA
    ....16398 bp total

    Extension    Content        Format
    ------------------------------------------
    Protein database formatted without "-o T"

    phr        deflines         binary

    pin        indices          binary

    psq        sequence data    binary

    Protein database formatted with "-o T" add these ISAM files:

    pnd        GI data          binary

    pni        GI indices       binary

    psd        non-GI data      binary

    psi        non-GI indices   binary

    N.B.: The pre-formatted protein BLAST databases distributed by NCBI
    (nr.*tar.gz and pataa.*tar.gz) contain a couple of extra files with the
    extensions .ppi and ppd. These are ISAM index and data files for looking
    up entries in the database using PIG as they key (see fastacmd -P option).
    These files cannot be generated by the stand alone formatdb binary included in
    this distribution.

    The formatdb index files involving deflines are large relative to the
    source database due to entries such as the one below in which the
    defline is much longer than the sequence.

    >gi|229659|pdb|1AAP|A Chain A, Protease Inhibitor Domain Of Alzheimer's
    Amyloid Beta-Protein Precursor (APPI)gi|229660|pdb|1AAP|B Chain B,
    Protease Inhibitor Domain Of Alzheimer's Amyloid Beta-Protein Precursor
    (APPI)
    VREVCSEQAETGPCRAMISRWYFDVTEGKCAPFFYGGCGGNRNNFDTEEYCMAVCGSA

    DISCLAIMER: The internal structure of the BLAST databases is subject
    to change with little or no notice.  The readdb API should be
    used to extract data from the BLAST databases.  Readdb is part
    of the NCBI toolkit (ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/),
    readdb.h contains a list of supported function calls.

    Last updated August 10 2006