IDFETCH(1)						     NCBI Tools User's Manual							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 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
	      8      FASTA reverse complement

AUTHOR

       The National Center for Biotechnology Information.

NCBI
								    2011-09-02								IDFETCH(1)