NAME

       epestfind - Finds PEST motifs as potential proteolytic cleavage sites

SYNOPSIS

       epestfind -sequence sequence [-mwdata datafile] -window integer -order selection
                 [-threshold float] -mono boolean -potential boolean -poor boolean
                 -invalid boolean -map boolean -outfile outfile -graph xygraph

       epestfind -help

DESCRIPTION

       epestfind is a command line program from EMBOSS (“the European Molecular Biology Open
       Software Suite”). It is part of the "Protein:Motifs" command group(s).

OPTIONS

   Input section
       -sequence sequence
           Protein sequence USA to be analysed.

       -mwdata datafile
           Default value: Emolwt.dat

   Required section
       -window integer
           Minimal distance between positively charged amino acids. Default value: 10

       -order selection
           Name of the output file which holds the results of the analysis. Results may be sorted
           by length, position and score. Default value: score

   Additional section
       -threshold float
           Threshold value to discriminate weak from potential PEST motifs. Valid PEST motifs are
           discriminated into 'poor' and 'potential' motifs depending on this threshold score. By
           default, the default value is set to +5.0 based on experimental data. Alterations are
           not recommended since significance is a matter of biology, not mathematics. Default
           value: +5.0

   Advanced section
       -mono boolean
           Default value: N

       -potential boolean
           Decide whether potential PEST motifs should be printed. Default value: Y

       -poor boolean
           Decide whether poor PEST motifs should be printed. Default value: Y

       -invalid boolean
           Decide whether invalid PEST motifs should be printed. Default value: N

       -map boolean
           Decide whether PEST motifs should be mapped to sequence. Default value: Y

   Output section
       -outfile outfile
           Name of file to which results will be written.

       -graph xygraph

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

       epestfind 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.