IDFETCH(1)

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 val

ues 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 inter

est

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.

NCBI 2007-10-19 IDFETCH(1)