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