fasta3x.me

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

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\fBCOPYRIGHT NOTICE\fP
.lp
Copyright 1988, 1991, 1992, 1994, 1995, 1996, 1999 by William
R. Pearson and the University of Virginia.  All rights reserved. The
FASTA program and documentation may not be sold or incorporated into a
commercial product, in whole or in part, without written consent of
William R. Pearson and the University of Virginia.  For further
information regarding permission for use or reproduction, please
contact: David Hudson, Assistant Provost for Research, University of
Virginia, P.O. Box 9025, Charlottesville, VA 22906-9025, (434)
924-6853
.uh "\s+2The FASTA program package\s0"
.uh "Introduction"
.pp
This documentation describes the version 3 of the FASTA program
package (see W. R. Pearson and D. J. Lipman (1988), "Improved Tools
for Biological Sequence Analysis", PNAS 85:2444-2448 [.wrp881.]; W. R.
Pearson (1996) "Effective protein sequence comparison"
Meth. Enzymol. 266:227-258;[.wrp960.] Pearson et. al. (1997) Genomics
46:24-36;[.wrp971.]  Pearson, (1999) Meth. in Molecular Biology
132:185-219.[.wrp000.]  Version 3 of the FASTA packages contains many
programs for searching DNA and protein databases and one program
(prss3) for evaluating statistical significance from randomly shuffled
sequences.  Several additional analysis programs, including programs
that produce local alignments, are available as part of version 2 of
the FASTA package, which is still available.
.pp
This document is divided into three sections: (1) A summary overview of
the programs in the FASTA3 package; (2) A guide to installing the
programs and databases; (3) A guide to using the FASTA programs. The
revision history of the programs can be found in the
\fCreadme.v30..v34\fP, files. The programs are easy to use, so if
you are using them on a machine that is administered by someone else,
you can skip section (2) and focus on (1) and (3) to learn how to use
the programsIf you are installing the programs on your own
machine, you will need to read section (2) carefully.
.sh 1 "An overview of the \f(CBFASTA\fP programs"
.pp
Although there are a large number of programs in this package, they
belong to three groups: (1) 
"Conventional" Library search programs:
FASTA3, FASTX3, FASTY3, TFASTA3, TFASTX3, TFASTY3, SSEARCH3;
(2)
Programs for searching with short fragments:
FASTS3, FASTF3, TFASTS3, TFASTF3;
(3)
Statistical significance: PRSS3.
Programs that start with \f(CBfast\fP search protein
databases, while \f(CBtfast\fP programs search translated DNA databases.
Table I gives a brief description of the programs.
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\d\fBTable I. Comparison programs in the FASTA3 package\fP\u

\fCfasta3\fP	T{
Compare a protein sequence to a protein sequence 
database or a DNA sequence to a DNA sequence database using the FASTA 
algorithm.[.wrp881,wrp960.]  Search speed and selectivity are 
controlled with the \fIktup\fP(wordsize) parameter.  For protein 
comparisons, \fIktup\fP = 2 by default; \fIktup\fP =1 is more sensitive 
but slower.  For DNA comparisons, \fIktup\fP=6 by default; \fIktup\fP=3 or 
\fIktup\fP=4 provides higher sensitivity; \fIktup\fP=1 should be used for 
oligonucleotides (DNA query lengths < 20).
T}

\fCssearch3\fP	T{
Compare a protein sequence to a protein sequence 
database or a DNA sequence to a DNA sequence database using the 
Smith-Waterman algorithm.[.wat815.]  \fCssearch3\fP is about 10-times 
slower than FASTA3, but is more sensitive for full-length protein 
sequence comparison.
T}

\fCfastx3\fP/ \fCfasty3\fP	T{
Compare a DNA sequence to a protein
sequence database, by comparing the translated DNA sequence in three
frames and allowing gaps and frameshifts.  \fCfastx3\fP uses a
simpler, faster algorithm for alignments that allows frameshifts only
between codons; \fCfasty3\fP is slower but produces better alignments
with poor quality sequences because frameshifts are allowed within
codons.
T}

\fCtfastx3\fP/ \fCtfasty3\fP	T{
Compare a protein sequence to a DNA sequence
database, calculating similarities with frameshifts to the forward and
reverse orientations.
T}

\fCtfasta3\fP	T{
Compare a protein sequence to a DNA sequence database, calculating 
similarities (without frameshifts) to the 3 forward and three reverse 
reading frames.  \fCtfastx3\fP and \fCtfasty3\fP are preferred because 
they calculate similarity over frameshifts.
T}

\fCfastf3/tfastf3\fP	T{
Compares an ordered peptide mixture, as would be obtained by
Edman degredation of a CNBr cleavage of a protein, against a protein
(\fCfastf\fP) or DNA (\fCtfastf\fP) database.
T}

\fCfasts3/tfasts3\fP	T{
Compares set of short peptide fragments, as would be obtained
from mass-spec. analysis of a protein, against a
protein (\fCfasts\fP) or DNA (\fCtfasts\fP) database.
T}
=	=
.TE
.)z
.sh 1 "Installing FASTA and the sequence databases"
.sh 2 "Obtaining the libraries"
.pp
The FASTA program package does not include any protein or DNA sequence
libraries.  Protein databases are available on CD-ROM from the PIR and
EMBL (see below), or via anonymouse FTP from many different sources.
As this document is updated in the fall of 1999, no DNA databases are
available on CD-ROM from the major sequence databases: Genbank at the
National for Biotechnology Information (\fCwww.ncbi.nlm.nih.gov\fP and
\fCftp://ncbi.nlm.nih.gov\fP) and EMBL at the European Bioinformatics
Institute (\fCwww.ebi.ac.uk\fP). However, the databases are available
via anonymous FTP from both sites.
.sh 3 "The GENBANK DNA sequence library"
.pp
Because of the large size of DNA databases, you will probably want to
keep DNA databases in only one, or possibly two, formats.  The FASTA3
programs that search DNA databases - \fCfasta3\fP, \fCtfastx/y3\fP,
and \fCtfasta3\fP can read DNA databases in Genbank flatfile (not
ASN.1), FASTA, GCG/compressed-binary, BLAST1.4 (\fCpressdb\fP), and
BLAST2.0 (\fCformatdb\fP) formats, as well as EMBL format.  If you are
also running the GCG suite of sequence analysis programs, you should
use GCG/compressed-binary format or BLAST2.0 format for your
\fCfasta3\fP searches.  If not, BLAST2.0 is a good choice.  These
files are considerably more compact than Genbank flat files, and are
preferred.  The NCBI does not provide software for converting from
Genbank flat files to Blast2.0 DNA databases, but you can use the
Blast \fCformatdb\fP program to convert ASN.1 formated Genbank files,
which are available from the NCBI \fCftp\fP site.
.pp
The NCBI also provides the \fCnr\fP, \fCswissprot\fP, and several EST
databases that are used by BLAST in FASTA format from:
\fCftp://ncbi.nlm.nih.gov/blast/db\fP.  These databases are updated
nightly.
.sh 3 "The NBRF protein sequence library"
.pp
You can obtain the PIR protein sequence database
[.pir980.] from:
.(l
National  Biomedical Research Foundation
Georgetown  University  Medical  Center
3900 Reservoir Rd, N.W.
Washington, D.C. 20007
.)l
or via ftp from \fCnbrf.georgetown.edu\fP or from the NCBI
(\fCncbi.nlm.nih.gov/repository/PIR\fP). The data in the \fCascii\fP
directory is in PIR Codata format, which is not widely used.  I
recommend the PIR/VMS format data (libtype=5) in the \fCvms\fP
directory.
.sh 3 "The EBI/EMBL CD-ROM libraries"
.pp
The European Bioinformatics Institute (EBI) distributes both the EMBL
DNA database and the SwissProt database on CD-ROM,[.apw961.] and they
are available from:
.(l
EMBL-Outstation  European Bioinformatics Institute
Wellcome Trust Genome Campus,
Hinxton Hall
Hinxton,
Cambridge CB10 1SD
United Kingdom
Tel: [phone]
Fax: [phone]
Email: [e-mail]
.)l
In addition, the SWISS-PROT protein sequence database is available via
anonymous FTP from \fCftp://ftp.expasy.ch/databases/swiss-prot/\fP
(also see \fCwww.expasy.ch\fP).
.sh 2 "Finding the libraries: FASTLIBS"
.pp
The major problem that most new users of the FASTA package have is in
setting up the program to find the databases and their library type.
In general, if you cannot get \fCfasta3\fP to read a sequence
database, it is likely that something is wrong with the \fCFASTLIBS\fP
file.  A common problem is that the database file is found, but either
no sequences are read, or an incorrect number of entries is read.
This is almost always because the library format (\fClibtype\fP) is
incorrect.  Note that a type 5 file (PIR/VMS format) can be read
as a type 0 (default FASTA) format file, and the number of entries
will be correct, but the sequence lengths will not.
.pp
All the search programs in the FASTA3 package use the environment
variable \fCFASTLIBS\fP to find the protein and DNA sequence libraries.  The
\fCFASTLIBS\fP variable contains the name of a file that has the actual
filenames of the libraries.  The \fCfastlibs\fP file included with the
distribution on is an example of a file that can be referred to by
FASTLIBS. To use the \fCfastlibs\fP file, type:
.(l
\fCsetenv FASTLIBS /usr/lib/fasta/fastgbs\fP (BSD UNIX/csh)
or
\fCexport FASTLIBS=/usr/lib/fasta/fastgbs\fP (SysV UNIX/ksh)
.)l
Then edit the \fCfastlibs\fP 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 \fC/usr/lib/aabank.lib\fP and
your Genbank DNA sequence library is kept in the directory:
\fC/usr/lib/genbank\fP, then \fCfastgbs\fP might contain:
.ne 8
.(l
.ft C
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$1M@/usr/lib/genbank/gmammal.nam
^   1    ^^^^       4                   ^     ^
          23                             (5)
.ft R
.)l
The first line of this file says that there is a copy of the NBRF
protein sequence database (which is a protein database) that can be
selected by typing "P" on the command line or when the database menu
is presented in the file \fC/usr/lib/seq/aabank.lib\fP.
.pp
Note that there are 4 or 5 fields in the lines in \fCfastgbs\fP.  The first
field is the description of the library which will be displayed by
FASTA; it ends with a '$'.  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.
.pp
The fourth field is the name of the library file.  In the example
above, the \fC/usr/lib/seq/aabank.lib\fP file contains the entire
protein sequence library.  However the DNA library file names are
preceded by a '@', because these files (\fCgpri.nam, grod.nam,
gmammal.nam\fP) 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.
.pp
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 \fCaabank.lib\fP file is
in Pearson/FASTA format, while the \fCswiss.seq\fP file is in PIR/VMS format
(from the EMBL CD-ROM). Currently, FASTA can read the following formats:
.(l I
.ft C
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)
12 NCBI Blast2.0 format  (unix only, fasta32t08 or later)
.ft R
.)l
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 specify a library type on the command line,
add it to the library filename and surround the filename and library
type in quotes:
.(l
.ft C
fasta3 query.file "/seqdb/genbank/gbpri1.seq 1"
.ft P
.)l
.pp
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: