
                              EMBOSS: prophet
     _________________________________________________________________
   
                                Program prophet
                                       
Function

   Gapped alignment for profiles
   
Description

   prophet finds matches between a GRIBSKOV or HENIKOFF profile produced
   by prophecy and one or more sequences.
   
   Note: prophet does NOT use the 'simple frequency matrices' produced by
   prophecy. If you have a 'simple frequency matrix'you should use the
   program profit to scan sequences.
   
Usage

   Here is a sample session with prophet.
   
(The sequence alignment looks like:)
% more m.seq
>one
DEVGGEA-GRLLVVYPWTQR
>two
DEVGREALGRLL-VYPWTQR
>three
DEVGGEALGRILVVY-WTQR
>four
DEVGGEAAGRVLVVYPWTQR

(Create the profile:)
% prophecy
Creates matrices/profiles from multiple alignments
Input sequence set: m.seq
Profile type
         F : Frequency
         G : Gribskov
         H : Henikoff
Select type [F]: g
Enter a name for the profile [mymatrix]:
Scoring matrix [Epprofile]:
Gap opening penalty [3.0]:
Gap extension penalty [0.3]:
Output file [outfile.prophecy]:

(Now do the search:)
% prophet
Gapped alignment for profiles
Input sequence(s): sw:*
Profile or matrix file: outfile.prophecy
Gap opening coefficient [1.0]:
Gap extension coefficient [0.1]:
Output file [100k_rat.prophet]:

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-infile]            infile     Profile or matrix file
   -gapopen            float      Gap opening coefficient
   -gapextend          float      Gap extension coefficient
  [-outfile]           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 database USA Readable sequence(s) Required
   [-infile]
   (Parameter 2) Profile or matrix file Input file Required
   -gapopen Gap opening coefficient Any integer value 1.0
   -gapextend Gap extension coefficient Any integer value 1.0
   [-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

   It reads a GRIBSKOV or a HENIKOFF profile produced by prophecy and
   searches one or more sequences.
   
Output file format

   The output of the above example follows:
   
Local: Consensus vs 100K_RAT
Score: 161.00

Consensus       1        DEV.G.GEALG.RLLVVYPWTQ                        19
                         |:: : ::||| ||:  ||::|
100K_RAT        479      DPLPAHRQALGERLY..YPRVQ                        498
Local: Consensus vs 104K_THEPA
Score: 138.25

Consensus       1        D.EVGGEAL.GRLLVVY.PWTQR                       20
                         : ||:::|  |  :|:: |::::
104K_THEPA      160      KYEVETHAKNGANMVTFIPRNGH                       182
Local: Consensus vs 108_LYCES
Score: 107.50

Consensus       1        DEVGGEAL.GRLLV.VYP..WTQ                       19
                         ::::| :: :::|| : |  :|:
108_LYCES       43       ASLTGLNVCAPFLVPGSPTASTE                       65
Local: Consensus vs 10KD_VIGUN
Score: 153.25

Consensus       1        DE.V.GGEA.LGRLLV.VY..P.WT                     18
                         :| | ::|| ::  || :|  | :|
10KD_VIGUN      20       QEVVVQSEAKTCENLVDTYRGPCFT                     44
Local: Consensus vs 110K_PLAKN
Score: 123.00

Consensus       1        DEVGGEALGRLLV..VYPW.TQ                        19
                         || ::::::  :|  | :  ||
110K_PLAKN      55       DENDEDEMTEQMVEEVADHITQ                        76
Local: Consensus vs 11S3_HELAN
Score: 156.50

Consensus       1        D..EV.GGEALGRLLVVY.PWTQR                      20
                         :  || ::|| : :  :: :::|:
11S3_HELAN      41       EPIEVIQAEAGV.VTEIWDAYDQQ                      63

etc.

Data files

   None.
   
Notes

   None.
   
References

   None.
   
Warnings

   prophet does NOT use the 'simple frequency matrices' produced by
   prophecy. If you have a 'simple frequency matrix'you should use the
   program profit to scan sequences.
   
Diagnostic Error Messages

   If you see something like:
   
   EMBOSS An error in prophet.c at line 110:
Unrecognised profile/matrix file format

   then you have probably given prophet a 'simple frequency matrix' and
   not a a GRIBSKOV or HENIKOFF profile produced by prophecy.
   
   If you see something like:
   
Uncaught exception
Allocation Failed
raised at prophet.c:147

   then you have run out of memory. This will occur if your sequence
   and/or your profile are large.
   
   prophet
   allocates space based on the length of the sequence and the size of
   the profile (8 x seqlen x profilelen)
   
Exit status

   It exists with a status of 0.
   
Known bugs

   None.
   
See also

   Program name                     Description
   profit       Scan a sequence or database with a matrix or profile
   prophecy     Creates matrices/profiles from multiple alignments
   
Author(s)

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

   Written (1999) - author - Alan Bleasby
   
Target users

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