EMBOSS: prophet

Program prophet ( YMBC , NCHC )

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

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

Written (1999) - author - Alan Bleasby

Target users

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

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