EMBOSS: prophet

Program prophet

Function

Gapped alignment for profiles

Description

Usage

Here is a sample session with prophet. 

% prophet

Command line arguments 

   Mandatory qualifiers:
  [-infile]            infile     Profile or matrix file
   -gapopen            float      Gap opening coefficient
   -gapextend          float      Gap extension coefficient
  [-sequence]          seqall     Sequence database USA
  [-outfile]           outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default
[-infile]
(Parameter 1)		 Profile or matrix file Input file Required
-gapopen Gap opening coefficient Any integer value 1.0
-gapextend Gap extension coefficient Any integer value 0.1
[-sequence]
(Parameter 2)		 Sequence database USA Readable sequence(s) Required
[-outfile]
(Parameter 3)		 Output file name Output file <sequence>.prophet
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 nameDescription
profitScan a sequence or database with a matrix or profile
prophecyCreates matrices/profiles from multiple alignments

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