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EFETCH(1) General Commands Manual EFETCH(1)

NAME

efetch - retrieve entries from sequence databases.

SYNOPSIS

efetch -options [database:]<query>

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.

DATABASES

SWissprot/SP, PIR, WOrmpep/WP, EMbl, GEnbank/GB, ProDom, ProSite

OPTIONS:

-a Search with Accession number
-f Fasta format output
-q Sequence only output (one line)
-s <#> Start at position #
-e <#> Stop at position #
-o More options and info...
-D <dir> Specify database directory
-H Display index header data
-p Display entrynames in search path
-r Print sequence in 'raw' format
-m Fetch from mixed mini database
-M Mini format output
-b Do NOT reverse the order of bytes (SunOS, IRIX do reverse, Alpha not)
-d <dbfile> Specify database file (avoid this)
-i <idxfile> Specify index file (avoid this)
-l <divfile> Specify division lookup table (avoid this)
-B <database> Specify database (archaic)
-A Only return entryname for accession number
-n <name> Give the sequence this name
-x Don't require query to match entry's name exactly (avoid)
-w For Wormpep: also fetch cross-referenced SwissProt entry
-h shows this help text

ENVIRONMENT

SWDIR = SwissProt directory - database and EMBL index files PIRDIR = PIR -- " -- WORMDIR = Wormpep -- " -- EMBLDIR = EMBL -- " -- GBDIR = Genbank -- " -- PRODOMDIR = ProDom -- " -- PROSITEDIR = ProSite -- " -- DBDIR = User's own -- " -- (fasta format)
SEQDB
database file (default SwissProt)
SEQDBIDX index file DIVTABL division lookup table
Ex. setenv DBDIR /pubseq/seqlibs/embl/
Note that Prodom family consensus seqs can be fetched by PD:_#

AUTHOR

Erik Sonnhammer (esr@sanger.ac.uk)
July 2010