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JASPSCAN(1e) EMBOSS Manual for Debian JASPSCAN(1e)


jaspscan - Scans DNA sequences for transcription factors


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

jaspscan -help


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).


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 can be reported to the Debian Bug Tracking system (, or directly to the EMBOSS developers (


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


Debian Med Packaging Team <>

Wrote the script used to autogenerate this manual page.


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.

05/11/2012 EMBOSS 6.4.0