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.