
                              EMBOSS: prophecy
     _________________________________________________________________
   
                               Program prophecy
                                       
Function

   Creates matrices/profiles from multiple alignments
   
Description

Usage

   Here is a sample session with prophecy.

% prophecy

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-sequence]          seqset     Sequence set USA
   -type               menu       Select type
   -name               string     Enter a name for the profile
*  -threshold          integer    Enter threshold reporting percentage
*  -datafile           matrixf    Scoring matrix
*  -open               float      Gap opening penalty
*  -extension          float      Gap extension penalty
  [-outf]              outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence set USA Readable sequences Required
   -type Select type
   F (Frequency)
   G (Gribskov)
   H (Henikoff)
   F
   -name Enter a name for the profile Any string is accepted mymatrix
   -threshold Enter threshold reporting percentage Integer from 1 to 100
   75
   -datafile Scoring matrix Comparison matrix file in EMBOSS data path
   'Epprofile' for Gribskov type, or EBLOSUM62
   -open Gap opening penalty Any integer value 3.0
   -extension Gap extension penalty Any integer value 0.3
   [-outf]
   (Parameter 2) Output file name Output file <sequence>.prophecy
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

Output file format

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

   Program name                     Description
   profit       Scan a sequence or database with a matrix or profile
   prophet      Gapped alignment for profiles
   
Author(s)

   This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)
   
History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
