efetch(1)
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:_#
