epestfind.ihelp

emboss的linux版本的源代码

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Protein sequence USA to be analysed.
   -window             integer    [10] Minimal distance between positively
                                  charged amino acids. (Integer 2 or more)
   -order              selection  [score] Name of the output file which holds
                                  the results of the analysis. Results may be
                                  sorted by length, position and score.
  [-outfile]           outfile    [*.epestfind] Name of file to which results
                                  will be written.
   -graph              xygraph    [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tekt, tek, none, data, xterm, png)

   Additional (Optional) qualifiers:
   -aadata             datafile   [Eamino.dat] Amino acids properties and
                                  molecular weight data file
   -threshold          float      [+5.0] 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. (Number from -55.00 to 55.00)

   Advanced (Unprompted) qualifiers:
   -[no]potential      boolean    [Y] Decide whether potential PEST motifs
                                  should be printed.
   -[no]poor           boolean    [Y] Decide whether poor PEST motifs should
                                  be printed.
   -invalid            boolean    [N] Decide whether invalid PEST motifs
                                  should be printed.
   -[no]map            boolean    [Y] Decide whether PEST motifs should be
                                  mapped to sequence.

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   "-graph" associated qualifiers
   -gprompt            boolean    Graph prompting
   -gdesc              string     Graph description
   -gtitle             string     Graph title
   -gsubtitle          string     Graph subtitle
   -gxtitle            string     Graph x axis title
   -gytitle            string     Graph y axis title
   -goutfile           string     Output file for non interactive displays
   -gdirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages