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

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.