prophecy

 

Function

Creates matrices/profiles from multiple alignments

Description

This creates a profile matrix file from a nucleic acid or a protein sequence alignment.

The profile matrix file can then be used by profit or prophet.

Usage

Here is a sample session with prophecy.

% prophecy
Creates matrices/profiles from multiple alignments
Input sequence set: globins.msf
Profile type
         F : Frequency
         G : Gribskov
         H : Henikoff
Select type [F]: 
Enter a name for the profile [mymatrix]: globins
Enter threshold reporting percentage [75]: 
Output file [globins.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                boolean    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 numeric value 3.0
-extension Gap extension penalty Any numeric 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

The input is a protein or a nucleic sequence alignment.

The one used in the example is:


!!AA_MULTIPLE_ALIGNMENT 1.0

  ../data/globins.msf MSF:  164 Type: P 25/06/01 CompCheck: 4278 ..

  Name: HBB_HUMAN Len: 164  Check: 6914 Weight: 0.14
  Name: HBB_HORSE Len: 164  Check: 6007 Weight: 0.15
  Name: HBA_HUMAN Len: 164  Check: 3921 Weight: 0.15
  Name: HBA_HORSE Len: 164  Check: 4770 Weight: 0.19
  Name: MYG_PHYCA Len: 164  Check: 7930 Weight: 0.23
  Name: GLB5_PETMA Len: 164  Check: 1857 Weight: 0.21
  Name: LGB2_LUPLU Len: 164  Check: 2879 Weight: 0.10

//

           1                                               50
HBB_HUMAN  ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR
HBB_HORSE  ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR
HBA_HUMAN  ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS
HBA_HORSE  ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG
MYG_PHYCA  ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE
GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE
LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD

           51                                             100
HBB_HUMAN  FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE
HBB_HORSE  FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE
HBA_HUMAN  FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
HBA_HORSE  FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD
MYG_PHYCA  KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ
GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD
LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN

           101                                            150
HBB_HUMAN  LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA
HBB_HORSE  LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA
HBA_HUMAN  LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS
HBA_HORSE  LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS
MYG_PHYCA  SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR
GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA
LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA

           151        164
HBB_HUMAN  NALAHKYH~~~~~~
HBB_HORSE  NALAHKYH~~~~~~
HBA_HUMAN  TVLTSKYR~~~~~~
HBA_HORSE  TVLTSKYR~~~~~~
MYG_PHYCA  KDIAAKYKELGYQG
GLB5_PETMA Y~~~~~~~~~~~~~
LGB2_LUPLU IVIKKEMNDAA~~~ 

Output file format

The output is a profile file.

The one produced by the above example is:


# Pure Frequency Matrix
# Columns are amino acid counts A->Z
# Rows are alignment positions 1->n
Simple
Name		globins
Length		164
Maximum score	496
Thresh		75
Consensus	PIVDTGSVVALSEEEKSAVDAAWVKANAVAEVGGHALERGLLALEPATLEFFDSFKDLSTFDASHGSAQVKAHGKKVLDALGAAVAHLDDLEGTLAALSDLHADKLHKGVDPVNFKLLSEALLVTLAAHFGADFTPEVQASLDKALAGVANVLAHKYHDAAYQG
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0  0  0  0  0  0  0  2  0  0  2  0  2  1  0  0  0  0  0  0  0  0  0  0  0  0  0  
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0  0  0  0  0  0  1  6  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
1  0  0  0  0  0  5  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
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0  0  0  0  0  1  0  0  0  0  4  0  0  0  0  0  0  1  0  1  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  1  0  1  0  0  0  0  0  0  0  0  0  0  5  0  0  0  0  0  
1  0  0  0  0  0  1  0  1  0  0  4  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
0  0  0  2  0  0  1  1  0  0  0  0  0  1  0  0  0  0  0  1  0  1  0  0  0  0  0  
5  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  1  0  0  
0  0  0  0  1  2  0  0  0  0  0  3  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  
1  0  0  0  0  0  2  0  0  0  0  0  0  1  0  0  0  0  1  2  0  0  0  0  0  0  0  
2  0  0  2  1  0  0  0  0  0  0  1  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  
3  0  0  0  0  0  2  0  2  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  0  0  0  2  0  0  0  0  1  0  0  0  0  4  0  0  0  0  0  
3  0  0  0  0  0  1  1  0  0  1  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  4  0  0  1  0  0  0  0  0  1  0  1  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  0  0  1  3  1  0  0  0  0  0  0  0  0  2  0  0  0  0  0  
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0  0  0  3  0  0  1  1  0  0  0  0  0  2  0  0  0  0  0  0  0  0  0  0  0  0  0  
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0  0  0  0  2  0  0  0  0  0  2  0  0  0  0  2  0  0  0  0  0  1  0  0  0  0  0  
1  0  0  0  0  0  3  0  0  0  1  0  0  1  0  0  0  0  0  0  0  1  0  0  0  0  0  
2  0  0  0  1  0  0  0  0  0  0  0  1  0  0  0  0  0  0  3  0  0  0  0  0  0  0  
0  0  0  1  0  2  0  0  0  0  0  3  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  
3  0  0  0  0  0  0  0  0  0  1  0  1  0  0  0  0  0  2  0  0  0  0  0  0  0  0  
2  0  0  0  0  0  0  0  0  0  1  0  0  1  0  1  0  0  0  2  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  0  0  0  7  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
1  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  1  4  0  0  0  0  0  0  0  0  
0  0  0  3  2  0  0  0  0  0  0  0  0  1  0  0  1  0  0  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  0  0  0  6  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  1  5  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  
3  0  2  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  
0  0  0  2  0  0  0  2  0  0  1  0  0  0  0  0  0  0  0  1  0  1  0  0  0  0  0  
0  0  0  0  0  0  0  2  0  0  5  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
1  0  0  0  0  0  0  1  0  0  0  4  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  
0  0  0  0  0  0  0  2  0  0  2  0  0  0  0  0  0  2  1  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  1  0  0  5  0  0  0  0  0  
1  0  0  4  0  1  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  
0  0  0  1  0  0  0  0  1  0  0  0  0  0  0  4  1  0  0  0  0  0  0  0  0  0  0  
1  0  0  0  2  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  3  0  0  0  0  0  
0  0  0  1  0  0  0  1  0  0  0  0  0  4  0  0  0  0  0  0  0  0  0  0  1  0  0  
0  0  0  0  0  5  0  0  0  0  0  1  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  
0  0  0  0  1  0  0  0  0  0  2  0  0  0  0  1  1  2  0  0  0  0  0  0  0  0  0  
0  0  0  0  0  1  0  0  0  0  0  4  0  0  0  0  0  0  0  0  0  1  0  0  1  0  0  
0  0  0  0  0  1  0  0  1  0  0  4  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  
0  0  0  0  0  0  2  0  0  0  2  0  0  0  0  0  0  0  3  0  0  0  0  0  0  0  0  
0  0  0  0  2  0  0  2  0  0  0  0  0  2  0  0  0  0  0  0  0  1  0  0  0  0  0  
2  0  2  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  2  0  0  0  0  0  
1  0  0  0  0  0  0  0  2  0  0  4  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
1  0  0  0  0  0  0  0  1  0  0  3  0  0  0  0  0  0  0  0  0  2  0  0  0  0  0  
0  0  1  0  0  0  0  1  0  0  1  0  0  0  0  0  0  0  1  0  0  3  0  0  0  0  0  
0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  3  0  3  0  0  0  0  0  
1  0  0  0  0  0  0  0  1  0  0  5  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
4  0  0  1  0  0  0  1  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
1  0  0  0  1  0  0  1  0  0  0  0  0  0  0  0  0  1  1  1  0  1  0  0  0  0  0  
0  0  0  0  0  0  0  4  0  0  0  0  0  0  0  0  0  1  0  0  0  2  0  0  0  0  0  
1  0  0  0  0  2  0  1  0  0  0  2  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  
1  0  0  0  0  0  3  0  0  0  0  0  0  0  0  3  0  0  0  0  0  0  0  0  0  0  0  
2  0  0  0  0  0  2  0  0  0  2  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  
0  0  0  4  2  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
1  0  0  0  0  5  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  
0  0  0  0  0  0  2  0  0  0  0  0  0  0  0  0  0  0  1  4  0  0  0  0  0  0  0  
1  0  0  0  1  1  0  0  0  0  0  0  0  0  0  4  0  0  0  0  0  0  0  0  0  0  0  
2  0  0  1  3  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  
1  0  0  0  0  0  0  0  0  0  1  2  0  0  0  0  0  0  0  0  0  3  0  0  0  0  0  
0  0  0  0  0  0  0  2  0  0  0  1  0  1  0  0  3  0  0  0  0  0  0  0  0  0  0  
4  0  0  0  0  0  1  0  0  0  0  0  1  0  0  0  0  0  1  0  0  0  0  0  0  0  0  
3  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  4  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  0  0  0  2  2  0  0  0  0  0  0  0  0  0  1  0  2  0  0  
0  0  0  2  0  0  0  0  1  0  0  0  0  1  0  0  2  0  0  1  0  0  0  0  0  0  0  
0  0  1  0  0  0  0  0  1  0  5  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
2  0  0  0  0  2  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  2  0  0  0  0  0  
0  0  0  0  0  0  0  0  0  0  0  4  0  0  0  0  0  0  0  0  0  2  0  0  1  0  0  
3  0  0  1  1  0  0  0  0  0  0  1  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  
0  0  0  0  1  0  2  0  0  0  0  1  0  0  0  0  0  1  2  0  0  0  0  0  0  0  0  
0  0  0  0  0  1  0  0  0  0  0  1  0  0  0  0  0  0  1  0  0  4  0  0  0  0  0  
4  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  2  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  1  0  1  0  0  2  0  0  0  0  0  2  0  0  0  0  1  0  0  
2  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  3  0  0  0  0  0  
0  0  0  0  0  0  0  0  2  0  0  4  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
3  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  2  0  0  0  0  0  0  0  
1  0  0  0  0  0  0  2  0  0  1  0  0  0  0  0  0  0  2  0  0  0  0  0  0  0  0  
0  0  0  0  1  0  0  0  0  0  5  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  5  0  0  
0  0  0  0  0  0  0  2  0  0  1  0  0  1  0  0  0  2  0  0  0  0  0  0  0  0  0  
0  0  0  1  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
1  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
1  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  
0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  


Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
profitScan a sequence or database with a matrix or profile
prophetGapped alignment for profiles

Author(s)

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

History

1999 - Written Alan Bleasby.

Target users

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

Comments