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.