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.

EMBOSS 6.4.0                                       05/11/2012                                       JASPSCAN(1e)