
                                 prophecy 



Function

   Create frequency matrix or profile from a multiple alignment

Description

   prophecy generates for an input sequence alignment a simple frequency
   matrix (for use by profit) or a position specific weighted profile
   using either the Gribskov (1) or Henikoff (2) method (for use by
   prophet). For constructing a simple frequency matrix, a residue
   substitution matrix, gap opening and gap extension penalty must be
   specified.

Algorithm

   The Gribskov scoring scheme is based on a notion of distance between a
   sequence and an ancestral or generalized sequence. For Henikoff it is
   based on weights of the diversity observed at each position in the
   alignment, rather than on a sequence distance measure.

Usage

   Here is a sample session with prophecy


% prophecy 
Create frequency matrix or profile from a multiple alignment
Input (aligned) 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]: 

   Go to the input files for this example
   Go to the output files for this example

   Example 2


% prophecy 
Create frequency matrix or profile from a multiple alignment
Input (aligned) sequence set: globins.msf
Profile type
         F : Frequency
         G : Gribskov
         H : Henikoff
Select type [F]: g
Scoring matrix [Epprofile]: 
Enter a name for the profile [mymatrix]: globins
Gap opening penalty [3.0]: 
Gap extension penalty [0.3]: 
Output file [globins.prophecy]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqset     (Aligned) sequence set filename and optional
                                  format, or reference (input USA)
   -type               menu       [F] Select type (Values: F (Frequency); G
                                  (Gribskov); H (Henikoff))
*  -datafile           matrixf    ['Epprofile' for Gribskov type, or
                                  EBLOSUM62] Scoring matrix
   -name               string     [mymatrix] Enter a name for the profile (Any
                                  string is accepted)
*  -threshold          integer    [75] Enter threshold reporting percentage
                                  (Integer from 1 to 100)
*  -open               float      [3.0] Gap opening penalty (Any numeric
                                  value)
*  -extension          float      [0.3] Gap extension penalty (Any numeric
                                  value)
  [-outfile]           outfile    [*.prophecy] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

   prophecy reads a protein or a nucleic sequence alignment USA.

  Input files for usage example

  File: globins.msf

!!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: 0.61
  Name: HBB_HORSE Len: 164  Check: 6007 Weight: 0.65
  Name: HBA_HUMAN Len: 164  Check: 3921 Weight: 0.65
  Name: HBA_HORSE Len: 164  Check: 4770 Weight: 0.83
  Name: MYG_PHYCA Len: 164  Check: 7930 Weight: 1.00
  Name: GLB5_PETMA Len: 164  Check: 1857 Weight: 0.91
  Name: LGB2_LUPLU Len: 164  Check: 2879 Weight: 0.43

//

           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.

  Output files for usage example

  File: globins.prophecy

# 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       PIVDTGSVVALSEEEKSAVDAAWVKANAVAEVGGHALERGLLALEPATLEFFDSFKDLSTFDA
SHGSAQVKAHGKKVLDALGAAVAHLDDLEGTLAALSDLHADKLHKGVDPVNFKLLSEALLVTLAAHFGADFTPEVQASL
DKALAGVANVLAHKYHDAAYQG
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  [Part of this file has been deleted for brevity]

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  Output files for usage example 2

  File: globins.prophecy

# Gribskov Protein Profile
# Columns are amino acids A->Z
# Last column is indel penalty
# Rows are alignment positions 1->n
Gribskov
Name            globins
Matrix          pprofile
Length          164
Max_score       939.76
Threshold       75
Gap_open        3.00
Gap_extend      0.30
Consensus       PIVDTGSVVSLSEEELSAVDKAWVKANSVAEVGGHALERGLFASEPMTLEFFDTFKYLSTFDL
SKGSADVKAHGKKVLDALGDAVAHLDDLEGTLAALSDLHAHKLKKGVDPVNFKLLSHCLLVVLASHLPGDFTPEVQASM
DKFLASVATVLASKYRELGYQG
0.65 0.00 0.13 0.13 0.13 -0.78 0.39 0.26 -0.26 0.00 0.13 -0.39 -0.26 0.00 0.00
1.95 0.39 0.39 0.52 0.39 0.00 0.13 -1.04 0.00 -1.04 0.00 0.87 0.87
0.00 0.00 0.26 -0.26 -0.26 0.78 -0.39 -0.39 1.95 0.00 -0.26 1.04 0.78 -0.39 0.0
0 -0.26 -0.39 -0.39 -0.13 0.26 0.00 1.43 -0.65 0.00 0.13 0.00 0.87 0.87
0.26 0.00 0.26 -0.26 -0.26 0.26 0.26 -0.39 1.43 0.00 -0.26 1.04 0.78 -0.39 0.00
 0.13 -0.26 -0.39 -0.13 0.26 0.00 1.95 -1.04 0.00 -0.13 0.00 0.87 0.87
0.39 0.00 -0.65 1.95 1.30 -1.30 0.78 0.52 -0.26 0.00 0.39 -0.65 -0.52 0.78 0.00
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  [Part of this file has been deleted for brevity]

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0.29 0.00 -0.86 0.86 0.86 -1.14 0.29 0.86 -0.43 0.00 0.57 -0.14 0.00 0.57 0.00
0.43 2.14 0.57 -0.14 -0.14 0.00 -0.29 -0.71 0.00 -0.86 0.00 0.92 0.92
0.86 0.00 0.29 0.86 0.71 -0.86 2.14 -0.29 -0.43 0.00 -0.14 -0.71 -0.43 0.57 0.0
0 0.43 0.29 -0.43 0.86 0.57 0.00 0.29 -1.43 0.00 -0.86 0.00 0.92 0.92

  Simple frequency matrix

   The columns represent amino acid counts for the amino acid residues
   from A to Z. The rows represent the alignment positions from 1->n. The
   file is a "Simple" frequency matrix of "Length" 20 amino acids. The
   maximum score this matrix can give is 496. The "Threshold" value is an
   instruction to the profit application to only report matches above the
   given score.

  Gribskov profile

   The columns represent the amino acids from A to Z, the rows denote the
   alignment position from 1 to n. The last column is the indel penalty.
   The "Name" is the name used by prophet to refer to the profile, the
   "Matrix" is the name of the scoring matrix used (containing residue
   substitution values). "Length" is the length of the alignment.
   "Max_score" is the maximum score this profile can produce. The
   threshold is an instruction to prophet to only report hits equal to or
   above the given value. The gap opening and extension values are used
   by prophet in the dynamic alignment (Smith Waterman equivalent).

Data files

   The two profile methods require a residue substitution scoring matrix.

   The Gribskov marices use the data file 'Epprofile' by default. This is
   derived from a PAM250 scoring matrix.

   The Henikoff matrices use the data file 'EBLOSUM62' by default.

   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by the EMBOSS
   environment variable EMBOSS_DATA.

   To see the available EMBOSS data files, run:

% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".

   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

Notes

   Profile analysis is a method for detecting distantly related proteins
   by sequence comparison. The basis for comparison is not only the
   customary Dayhoff mutational-distance matrix but also the results of
   structural studies and information implicit in the alignments of the
   sequences of families of similar proteins. This information is
   expressed in a position-specific scoring table (profile), which is
   created from a group of sequences previously aligned by structural or
   sequence similarity. The similarity of any other target sequence to
   the group of aligned probe sequences can be tested by comparing the
   target to the profile using dynamic programming algorithms. The
   profile method differs in two major respects from methods of sequence
   comparison in common use: (i) Any number of known sequences can be
   used to construct the profile, allowing more information to be used in
   the testing of the target than is possible with pairwise alignment
   methods. (ii) The profile includes the penalties for insertion or
   deletion at each position, which allow one to include the probe
   secondary structure in the testing scheme.

References

    1. Gribskov M, McLachlan AD, Eisenberg D. Proc Natl Acad Sci U S A.
       1987 Jul; 84(13): 4355-8.
    2. Henikoff S, Henikoff JG. J Mol Biol. 1994 Nov 4; 243(4): 574-8.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name                          Description
   profit       Scan one or more sequences with a simple frequency matrix
   prophet      Scan one or more sequences with a Gribskov or Henikoff profile

Author(s)

   Alan Bleasby (ajb  ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, 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

   None
