GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  IDFETCH (1)

NAME

idfetch - retrieve biological data from the NCBI ID1 server

CONTENTS

Synopsis
Description
Options
Author

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 \(aq5(HUMHBB)\(aq
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.
Search for    or go to Top of page |  Section 1 |  Main Index


NCBI IDFETCH (1) 2007-10-19

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.