---
name: "jaspscan"
section: "1e"
platform: "linux"
package: "emboss"
version: "6.6.0+dfsg-15"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/jaspscan"
---

# jaspscan(1e)

Scans DNA sequences for transcription factors

## NAME

jaspscan - Scans DNA sequences for transcription factors

## SYNOPSIS

**jaspscan** **-sequence** *seqall* **-menu** *list* **-matrices** *string* **-threshold** *float* \[**-exclude** *string*\] \[**-both** *boolean*\] **-outfile** *report*

**jaspscan** **-help**

## DESCRIPTION

**jaspscan** is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Nucleic:Transcription" command group(s).

## OPTIONS

### Input section

- **-sequence** *seqall*

  - **-menu** *list*

  Default value: C

- **-matrices** *string*

  The name 'all' reads in all matrix files from the selected JASPAR matrix set. You can specify individual matrices by giving their names with commas between then, such as: 'ma0001.1,ma0015\*'. The case of the names is not important. You can specify a file of matrix names to read in by giving the name of the file holding the matrix names with a '@' character in front of it, for example, '@matrix.list'. Blank lines and lines starting with a hash character or '!' are ignored and all other lines are concatenated together with a comma character ',' and then treated as the list of enzymes to search for. An example of a file of matrix names is: ! my matrices ma0001.1, ma0002.1 ! other matrices ma0010.1 ma0032\* ma0053.1 Default value: all

### Required section

- **-threshold** *float*

  If the matrix score is greater than or equal to this percentage then a hit will be reported Default value: 80.0

### Additional section

- **-exclude** *string*

  The names of any matrices to exclude from the 'matrices' list. Matrices are specified in the same way as for the selection list.

- **-both** *boolean*

  If set then both the forward and reverse strands are searched Default value: N

### Output section

- **-outfile** *report*

  ## BUGS

Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group\_id=93650&atid=605031).

## SEE ALSO

jaspscan is fully documented via the **tfm**(1) system.

## AUTHOR

**Debian Med Packaging Team** \<debian-med-packaging@lists.alioth.debian.org\>

Wrote the script used to autogenerate this manual page.

## COPYRIGHT

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.