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epestfind - Finds PEST motifs as potential proteolytic cleavage sites


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


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).


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

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