.\" This file was generated by help2man 1.37.1 with some additional
.\" manual editing.
.TH EFETCH "1" "July 2010" 
.SH NAME
efetch \- retrieve entries from sequence databases.
.SH SYNOPSIS
efetch \fB\-options\fR [database:]<query>
.SH DESCRIPTION
In the late 90s efetch was a very popular tool to extremely quickly retrieve 
entries from the most common public bioinformatics sequence and motif databases.
.SH DATABASES
SWissprot/SP, PIR, WOrmpep/WP, EMbl, GEnbank/GB, ProDom, ProSite
.SH OPTIONS:
\fB\-a\fR            Search with Accession number
.HP
\fB\-f\fR            Fasta format output
.HP
\fB\-q\fR            Sequence only output (one line)
.HP
\fB\-s\fR <#>        Start at position #
.HP
\fB\-e\fR <#>        Stop at position #
.HP
\fB\-o\fR            More options and info...
.HP
\fB\-D\fR <dir>
Specify database directory
.HP
\fB\-H\fR
Display index header data
.HP
\fB\-p\fR
Display entrynames in search path
.HP
\fB\-r\fR
Print sequence in 'raw' format
.HP
\fB\-m\fR
Fetch from mixed mini database
.HP
\fB\-M\fR
Mini format output
.HP
\fB\-b\fR
Do NOT reverse the order of bytes
(SunOS, IRIX do reverse, Alpha not)
.HP
\fB\-d\fR <dbfile>
Specify database file (avoid this)
.HP
\fB\-i\fR <idxfile>
Specify index file (avoid this)
.HP
\fB\-l\fR <divfile>
Specify division lookup table (avoid this)
.HP
\fB\-B\fR <database> Specify database (archaic)
.HP
\fB\-A\fR
Only return entryname for accession number
.HP
\fB\-n\fR <name>
Give the sequence this name
.HP
\fB\-x\fR
Don't require query to match entry's name exactly (avoid)
.HP
\fB\-w\fR
For Wormpep: also fetch cross\-referenced SwissProt entry
.HP
\fB\-h\fR
shows this help text
.SH ENVIRONMENT
SWDIR      = SwissProt  directory \- database and EMBL index files
PIRDIR     = PIR        \fB\-\-\fR " \fB\-\-\fR
WORMDIR    = Wormpep    \fB\-\-\fR " \fB\-\-\fR
EMBLDIR    = EMBL       \fB\-\-\fR " \fB\-\-\fR
GBDIR      = Genbank    \fB\-\-\fR " \fB\-\-\fR
PRODOMDIR  = ProDom     \fB\-\-\fR " \fB\-\-\fR
PROSITEDIR = ProSite    \fB\-\-\fR " \fB\-\-\fR
DBDIR      = User's own \fB\-\-\fR " \fB\-\-\fR (fasta format)
.TP
SEQDB
database file (default SwissProt)
.IP
SEQDBIDX index file
DIVTABL  division lookup table
.IP
Ex. setenv DBDIR /pubseq/seqlibs/embl/
.IP
Note that Prodom family consensus seqs can be fetched by PD:_#
.SH AUTHOR
Erik Sonnhammer (esr@sanger.ac.uk)