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efetch - Online in the Cloud

Run efetch in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command efetch that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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:_#

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