epestfind1e
Finds pest motifs as potential proteolytic cleavage sites
Usage
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
Overview
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
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.
-mono since Debian 6.0 (Squeeze);
-mwdata since Debian 6.0 (Squeeze).
-aadata until Debian 5.0 (Lenny).