afetch.man

hmmer源程序

.TH "afetch" 1 "@RELEASEDATE@" "@PACKAGE@ @RELEASE@" "@PACKAGE@ Manual"

.SH NAME
.TP 
afetch - retrieve an alignment from an alignment database 

.SH SYNOPSIS
.B afetch
.I [options]
.I alignmentdb
.I key

.PP
.B afetch --index
.I alignmentdb

.SH DESCRIPTION

.B afetch
retrieves the alignment named
.I key
from an alignment database in file
.I alignmentdb.

.PP 
.I alignmentdb 
is a "multiple multiple alignment" file in Stockholm (e.g. native
Pfam) format.

.PP
.I key 
is either the name (ID) of the alignment, or its accession
number (AC).

.PP
The 
.I alignmentdb
file should first be SSI indexed with
.B afetch --index
for efficient retrieval. An SSI index is
not required, but alignment retrieval without one may
be painfully slow.

.SH OPTIONS

.TP
.B -h
Print brief help; includes version number and summary of
all options, including expert options.

.SH EXPERT OPTIONS

.TP
.B --index
Instead of retrieving a
.I key,
the special command
.B afetch --index
.I alignmentdb
produces an SSI index of the names and accessions
of the alignments in 
the file 
.I alignmentdb. 
This should be run once on the 
.I alignmentdb
file to prepare it for all future afetch's.

.SH SEE ALSO

.PP
Master man page, with full list of and guide to the
individual man pages for SQUID's auxiliary programs: see
.B squid(1).

.SH AUTHOR

@PACKAGE@ and its documentation is @COPYRIGHT@
HMMER - Biological sequence analysis with profile HMMs
Copyright (C) 1992-1999 Washington University School of Medicine
All Rights Reserved

    This source code is distributed under the terms of the
    GNU General Public License. See the files COPYING and LICENSE
    for details.
See COPYING in the source code distribution for more details, or contact me.

.nf
Sean Eddy
Dept. of Genetics
Washington Univ. School of Medicine
4566 Scott Ave.
St Louis, MO 63110 USA
Phone: [phone]
FAX  : [phone]
Email: [e-mail]
.fi