efetch(1) retrieve entries from sequence databases.


efetch -options [database:]<query>


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.


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


-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
Display index header data
Display entrynames in search path
Print sequence in 'raw' format
Fetch from mixed mini database
Mini format output
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)
Only return entryname for accession number
-n <name>
Give the sequence this name
Don't require query to match entry's name exactly (avoid)
For Wormpep: also fetch cross-referenced SwissProt entry
shows this help text


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)
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:_#


Erik Sonnhammer ([email protected])