fasta20.doc

序列对齐 Compare a protein sequence to a protein sequence database or a DNA sequence to a DNA sequenc

option.  FASTA -r results.out ... creates a file with a list of
scores for every sequence in the library.  The list is not
sorted, and only includes those scores calculated during the
initial scan of the library.

2.  Installing the FASTA package

2.1.  Installing the programs

2.1.1.  Unix version

     The FASTA distribution comes with several makefile's that
can be used to compile the FASTA programs.  Over the years, as
ATT Unix System 5 and BSD unix have converged, these files have
become very similar. To begin with, I recommend using the
standard Makefile.  There are two values in the makefile that
should be checked against the values used on your system: the HZ
value, which is the frequency in ticks per second used by the
times() system call, this value can usually be found by running:

    grep HZ /usr/include/sys/*

and the functions available to return random numbers.  If you
have a rand48() function that returns a 32-bit random number, use
it and use the lines:

    NRAND=nrand48
    RANFLG= -DRAND32

If not, you will need to use the rand() function call and
determine whether it returns a 16-bit or a 32-bit value.  These
functions are used by PRDF and PRSS.  If you have problems
compiling the programs, you may want to examine the makefile.unx
and makefile.sun files, to look for differences.  I have tried to
use very standard unix functions in these programs, and they have
been successfully compiled, with very small changes to the
Makefile, on Sun's (Sun OS 4.1), IBM RS/6000's (AIX), and MIPS
machines (under the BSD environment).

2.1.2.  IBM-PC/DOS version

     For the IBM-PC/DOS version, the FASTA source code disk
contains the complete source code to all of the programs on the
other disks.  The programs were compiled with Borland's Turbo
'C++', using Borland's MAKE utility.  The graphics programs
(PLFASTA, TGREASE) use the graphics device drivers supplied with
the Turbo 'C' V2.0 package.  Also included are the documentation
files PROGRAMS.DOC and FORMAT.DOC.  You do not need any of the
files the source code disk to run the programs.  The files on
this disk are identical to the UNIX and VMS versions that run on
larger machines.  Also included is the code to compile
ALIGN0.EXE.  ALIGN0 is the same as ALIGN, but does not penalize
for end-gaps.

     If you have the DOS or Macintosh version of the FASTA
package, to install the programs you should:

 (1)   Make a new directory (folder) for the FASTA programs.
       This need not be the same as the directory for your
       sequence databases.

 (2)   Copy the files from the FASTA source disk to the new
       directory.

 (3)   (DOS only) Edit your AUTOEXEC.BAT file to (a) modify your
       PATH command to include the FASTA directory and (b) add
       the line:

           set FASTLIBS=c:\yourfastadirectory\fastgbs

       On the Macintosh, you may need to edit the "environment"
       file and change the line that reads:

           FASTLIBS=fastgbs

       to indicate the full directory path for the fastgbs file,
       for example:

           FASTLIBS=Q105:FASTA:fastgbs


 (4)   Finally, you will need to edit the fastgbs file.  This is
       usually the most confusing part of the installation.  An
       example of this file is shown below; to customize this
       file for your machine, you will need to change the file
       names from those provided in the fastgbs file to ones that
       reflect the directory names and file names you use on your
       machine. This is explained in more detail below.  In
       addition, some entries in the fastgbs file refer to other
       files of file names.  These files of file names (as
       opposed to actual database files) may also need to be
       edited.

2.2.  Installing the libraries

2.2.1.  The NBRF protein sequence library

     The FASTA program package does not include any protein or
DNA sequence libraries.  You can obtain the PIR protein sequence
database from:

    National  Biomedical Research Foundation
    Georgetown  University  Medical  Center
    3900 Reservoir Rd, N.W.
    Washington, D.C. 20007

In addition, this database is available via anonymous ftp from
the host "ftp.bchs.uh.edu". It is available in two formats, VMS
and CODATA format.  The "VMS" format (library type 5 below) can
be searched much faster, can be easily reformatted for use by the
"BLAST" rapid searching program, and is compatible with the
Genetics Computer Group package of programs.  The CODATA format
is used by the EUGENE/MBIR computing package from Baylor (library
type 2).

2.2.2.  The GENBANK DNA sequence library

     FASTA, and TFASTA search sequences from the GENBANK
"flatfile" (not ASN.1) DNA sequence library in the flat-file
format distributed by the National Center for Biotechnology
Information and the PIR format used by EBI/EMBL.  CD-ROMs can be
obtained from:

    Genbank
    National Center for Biotechnology Information
    National Library of Medicine
    National Institutes of Health
    8600 Rockville Pike
    Bethesda, MD  20894


     The GenBank DNA sequence library is also available via
anonymous FTP from ncbi.nlm.nih.gov.

2.2.3.  The EBI/EMBL CD-ROM libraries

     The European Bioinformatics Institute (EBI) is now
distributing the EMBL CD-ROM that contains both the complete EMBL
DNA sequence database (which should be essentially identical to
the GenBank DNA sequence database) and the SWISS-PROT protein
sequence database. SWISS-PROT is derived from the NBRF Protein
sequence database with additions from the EBI/EMBL DNA sequence
database.  This CD-ROM is a "best-buy," since it provides both
DNA and protein sequence libraries.  It is available from:


    European Bioinformatics Institute
    Hinxton Genome Campus, Hinxton Hall
    Hinxton, Cambridge CB10 1RQ,
    United Kingdom
    Tel: [phone]
    Fax: [phone]
    Email: [e-mail]



     In addition, the SWISS-PROT protein sequence database is
available via anonymous FTP from ncbi.nlm.nih.gov.

2.3.  Finding the libraries: FASTLIBS

     FASTA and TFASTA use the environment variable FASTLIBS to
find the protein and DNA sequence libraries.  The FASTLIBS
variable contains the name of a file that has the actual
filenames of the libraries.  The FASTGBS file on is an example of
a file that can be referred to by FASTLIBS. To use the FASTGBS
file, type:

    setenv FASTLIBS /usr/lib/fasta/fastgbs (BSD UNIX/csh)
    or
    export FASTLIBS=/usr/lib/fasta/fastgbs (SysV UNIX/ksh)

Then edit the FASTGBS file to indicate where the protein and DNA
sequence libraries can be found.  If you have a hard disk and
your protein sequence library is kept in the file
/usr/lib/aabank.lib and your Genbank DNA sequence library is kept
in the directory: /usr/lib/genbank, then fastgbs might contain:

    NBRF Protein$0P/usr/lib/seq/aabank.lib 0
    SWISS PROT 10$0S/usr/lib/vmspir/swiss.seq 5
    GB Primate$1P@/usr/lib/genbank/gpri.nam
    GB Rodent$1R@/usr/lib/genbank/grod.nam
    GB Mammal$1M@/usr/lib/genbank/gmammal.nam
    ^   1    ^^^^       4                   ^     ^
              23                             (5)

The first line of this file says that there is a copy of the NBRF
protein sequence database (which is a protein database) that can
be selected by typing "P" on the command line or when the
database menu is presented in the file /usr/lib/seq/aabank.lib.

     Note that there are 4 or 5 fields in the lines in fastgbs.
The first field is the description of the library which will be
displayed by FASTA; it ends with a '$'.  The second field (1
character), is a 0 if the library is a protein library and 1 if
it is a DNA library.  The third field (1 character) is the
character to be typed to select the library.

     The fourth field is the name of the library file.  In the
example above, the /usr/lib/seq/aabank.lib file contains the
entire protein sequence library.  However the DNA library file
names are preceded by a '@', because these files (gpri.nam,
grod.nam, gmammal.nam) do not contain the sequences; instead they
contain the names of the files which contain the sequences.  This
is done because the GENBANK DNA database is broken down in to a
large number of smaller files.  In order to search the entire
primate database, you must search more than a dozen files.

     In addition, an optional fifth field can be used to specify
the format of the library file.  Alternatively, you can specify
the library format in a file of file names (a file preceded by an
'@').  This field must be separated from the file name by a space
character (' ') from the filename.  In the example above, the
aabank.lib file is in Pearson/FASTA format, while the swiss.seq
file is in PIR/VMS format (from the EMBL CD-ROM). Currently,
FASTA can read the following formats:

    0 Pearson/FASTA (>SEQID - comment/sequence)
    1 Uncompressed Genbank (LOCUS/DEFINITION/ORIGIN)
    2 NBRF CODATA (ENTRY/SEQUENCE)
    3 EMBL/SWISS-PROT (ID/DE/SQ)
    4 Intelligenetics (;comment/SEQID/sequence)
    5 NBRF/PIR VMS (>P1;SEQID/comment/sequence)
    6 GCG (version 8.0) Unix Protein and DNA (compressed)
    11 NCBI Blast1.3.2 format  (unix only)

In particular, this version will work with the EMBL and PIR VMS
formats that are distributed on the EMBL CD-ROM. The latter
format (PIR VMS) is much faster to search than EMBL format.  This
release also works with the protein and DNA database formats
created for the BLASTP and BLASTN programs by SETDB and PRESSDB
and with the new NCBI search format.  If a library format is not
specified, for example, because you are just comparing two
sequences, Pearson/FASTA (format 0) is used by default.  To
change this default, you may set the LIBTYPE environment variable
to a number.  For example,

    setenv LIBTYPE 1

would cause the program to use the GenBank LOCUS format by
default for libraries (or the second sequence file), but the
Pearson/FASTA format would still be used for the query sequence.

     You can specify a group of library files by putting a '@'
symbol before a file that contains a list of file names to be
searched.  For example, if @gmam.nam is in the fastgbs file, the
file "gmam.nam" might contain the lines:

    </usr/lib/genbank
    gbpri.seq 1
    gbrod.seq 1
    gbmam.seq 1

In this case, the line beginning with a '<' indicates the
directory the files will be found in.  The remaining lines name
the actual sequence files.  So the first sequence file to be
searched would be:

    /usr/lib/genbank/gbpri.seq

The notation "<PIRNAQ:" might be used under the VAX/VMS operating
system. Under UNIX, the trailing '/' is left off, so the library
directory might be written as "</usr/seqlib".

     With version 1.4 of the FASTA package, the FASTA and TFASTA
programs can search a library composed of different files in
different sequence formats.  For example, you may wish to search
the Genbank files (in GenBank flat file format) and the EMBL DNA
sequence database on CD-ROM.  To do this, you simply list the
names and filetypes of the files to be searched in a file of
filenames.  For example, to search the mammalian portion of
Genbank, the unannotated portion of Genbank, and the unannotated
portion of the EMBL library, you could use the file:

    </usr/lib/DNA
    gbpri.seq 1
    #  (this '#' causes the program to display the size of the library)
    gbrod.seq 1
    gbmam.seq 1
    gbuna.seq 1
    unanno.seq 5
    #

    You do not need to include library format numbers if  you
    only use the Pearson/FASTA version of the PIR protein se-
    quence library.  If no library  type  is  specified,  the
    program  assumes  that  type  0 is being used (unless you