---
name: "idfetch"
section: "1"
platform: "linux"
package: "ncbi-tools-bin"
version: "6.1.20170106+dfsg2-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/idfetch"
---

# idfetch(1)

retrieve biological data from the NCBI ID1 server

## 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.