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 -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
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:_#
Erik Sonnhammer ([email protected])