NAME
idfetch - retrieve biological data from the NCBI ID1 server
SYNOPSIS
idfetch [-] [-F str] [-G filename] [-Q filename] [-c N] [-d str] [-e N]
[-f str] [-g N] [-i N] [-l filename] [-n] [-o filename] [-q str]
[-s str] [-t N]
DESCRIPTION
idfetch is a client for NCBI’s ID1 server, which contains a large
database of annotated biological sequences.
OPTIONS
A summary of options is included below.
- Print usage message
-F str Add the specified feature types (comma-delimited); allowed
values are CDD, SNP, SNP_graph, MGC, HPRD, STS, tRNA, and
microRNA.
-G filename
File with list of GIs, (versioned) accessions, FASTA SeqIDs to
dump
-Q filename
Generate GI list by Entrez query in filename; requires -dn or
-dp.
-c N Max complexity:
0 get the whole blob (default)
1 get the bioseq of interest
2 get the minimal bioseq-set containing the bioseq of
interest
3 get the minimal nuc-prot containing the bioseq of
interest
4 get the minimal pub-set containing the bioseq of interest
-d str Database to use (with -q, can be either n for nucleotides or p
for proteins).
-e N Entity number (retrieval number) to dump
-f str Flattened SeqId. Possible formats:
type([name][,[accession][,[release][,version]]]) as '5(HUMHBB)'
type=accession
type:number
(type is a number indicating the ASN.1 Seq-id subtype.)
-g N GI id for single Entity to dump
-i N Type of lookup:
0 get Seq-entry (default)
1 get GI state (output to stderr)
2 get SeqIds
3 get GI history (sequence change only)
4 get revision history (any change to ASN.1)
-l filename
Log file
-n Output only the list of GIs (with -q and -Q).
-o filename
Filename for output (default = stdout)
-q str Generate gi list by Entrez query. Requires -dn or -dp.
-s str FASTA style SeqId ENCLOSED IN QUOTES. Formats:
lcl|int or str
bbs|int
bbm|int
gb|acc|loc
emb|acc|loc
pir|acc|name
sp|acc|name
pat|country|patent|seq
gi|int
dbj|acc|loc
prf|acc|name
pdb|entry|chain
-t N Output type:
1 text ASN.1 (default)
2 binary ASN.1
3 GenBank (Seq-entry only)
4 GenPept (Seq-entry only)
5 FASTA (table for history)
6 quality scores (Seq-entry only)
7 Entrez DocSums
AUTHOR
The National Center for Biotechnology Information.