---
name: "ncbi_search"
section: "1"
platform: "linux"
package: "cct"
version: "1:1.0.3-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/ncbi_search"
---

# ncbi\_search(1)

visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences

## NAME

ncbi\_search - visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences

## DESCRIPTION

### USAGE:

-

  ncbi\_search **-q** STRING **-o** FILE **-d** STRING **-r** STRING \[Options\]

### DESCRIPTION:

-

  Uses NCBI's eSearch to download collections of sequences.

### REQUIRED ARGUMENTS:

**-q**, **--query** \[STRING\]

-

  Raw query text.

**-o**, **--output** \[FILE\]

-

  Output file to create. If the split option is given, this should be a directory, where the returned records will be written. If the directory does not exist it will be created.

**-d**, **--database** \[STRING\]

-

  Name of the NCBI database to search, such as 'nucleotide', 'protein', or 'gene'.

**-r**, **--return\_type** \[STRING\]

-

  The type of information requested. For sequences 'fasta' is often used. The accepted formats vary depending on the database being queried.

**-s**, **--split**

-

  Return each record as a separate file where the file name will will be the accesssion id of the record. This option only works if the return\_type is 'gb' or 'gbwithparts'.

**-m**, **--max\_records** \[INTEGER\]

-

  The maximum number of records to return (default is to return all matches satisfying the query).

**-v**, **--verbose**

-

  Provide progress messages.

**-h**, **--help**

-

  Show this message.

### EXAMPLE:

-

  ncbi\_search **-q** 'dysphagia AND homo sapiens\[ORGN\]' \\

**-o** results.txt **-d** pubmed **-r** uilist **-m** 100

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.