| ## 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