prophecy

 

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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 

Create frequency matrix or profile from a multiple alignment
Version: EMBOSS:6.6.0.0

   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)
*  -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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 and exit. 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
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-sequence]
(Parameter 1)		 seqset (Aligned) sequence set filename and optional format, or reference (input USA) Readable set of sequences Required
-type list Select type
F (Frequency)
G (Gribskov)
H (Henikoff)
 F
-datafile matrixf Scoring matrix Comparison matrix file in EMBOSS data path 'Epprofile' for Gribskov type, or EBLOSUM62
-name string Enter a name for the profile Any string mymatrix
-threshold integer Enter threshold reporting percentage Integer from 1 to 100 75
-open float Gap opening penalty Any numeric value 3.0
-extension float Gap extension penalty Any numeric value 0.3
[-outfile]
(Parameter 2)		 outfile Output file name Output file <*>.prophecy
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-sequence" associated seqset qualifiers
-sbegin1
-sbegin_sequence		 integer Start of each sequence to be used Any integer value 0
-send1
-send_sequence		 integer End of each sequence to be used Any integer value 0
-sreverse1
-sreverse_sequence		 boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_sequence		 boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_sequence		 boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_sequence		 boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_sequence		 boolean Make lower case Boolean value Yes/No N
-supper1
-supper_sequence		 boolean Make upper case Boolean value Yes/No N
-scircular1
-scircular_sequence		 boolean Sequence is circular Boolean value Yes/No N
-squick1
-squick_sequence		 boolean Read id and sequence only Boolean value Yes/No N
-sformat1
-sformat_sequence		 string Input sequence format Any string  
-iquery1
-iquery_sequence		 string Input query fields or ID list Any string  
-ioffset1
-ioffset_sequence		 integer Input start position offset Any integer value 0
-sdbname1
-sdbname_sequence		 string Database name Any string  
-sid1
-sid_sequence		 string Entryname Any string  
-ufo1
-ufo_sequence		 string UFO features Any string  
-fformat1
-fformat_sequence		 string Features format Any string  
-fopenfile1
-fopenfile_sequence		 string Features file name Any string  
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile		 string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

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	PIVDTGSVVALSEEEKSAVDAAWVKANAVAEVGGHALERGLLALEPATLEFFDSFKDLSTFDASHGSAQVKAHGKKVLDALGAAVAHLDDLEGTLAALSDLHADKLHKGVDPVNFKLLSEALLVTLAAHFGADFTPEVQASLDKALAGVANVLAHKYHDAAYQG
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  [Part of this file has been deleted for brevity]

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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

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	PIVDTGSVVSLSEEELSAVDKAWVKANSVAEVGGHALERGLFASEPMTLEFFDTFKYLSTFDLSKGSADVKAHGKKVLDALGDAVAHLDDLEGTLAALSDLHAHKLKKGVDPVNFKLLSHCLLVVLASHLPGDFTPEVQASMDKFLASVATVLASKYRELGYQG
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 0.00 -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 0.13 0.78 0.00 0.26 0.26 0.00 -0.26 -1.43 0.00 -0.65 0.00 0.87 0.87
0.52 0.00 0.26 0.26 0.26 -0.39 0.52 -0.13 0.26 0.00 0.26 -0.13 0.00 0.26 0.00 0.39 -0.13 -0.13 0.39 1.95 0.00 0.26 -0.78 0.00 -0.39 0.00 0.87 0.87
0.78 0.00 0.26 0.78 0.65 -0.78 1.95 -0.26 -0.39 0.00 -0.13 -0.65 -0.39 0.52 0.00 0.39 0.26 -0.39 0.78 0.52 0.00 0.26 -1.30 0.00 -0.78 0.00 0.87 0.87
0.52 0.00 0.78 0.26 0.26 -0.39 0.78 -0.26 -0.13 0.00 0.26 -0.52 -0.39 0.39 0.00 0.52 -0.13 0.13 1.95 0.39 0.00 -0.13 0.39 0.00 -0.52 0.00 0.87 0.87
0.55 0.00 0.55 -0.55 -0.55 0.55 0.55 -0.82 3.00 0.00 -0.55 2.18 1.64 -0.82 0.00 0.27 -0.55 -0.82 -0.27 0.55 0.00 4.09 -2.18 0.00 -0.27 0.00 0.87 0.87
2.54 0.00 -0.27 -0.32 -0.09 1.06 1.35 -1.08 2.94 0.00 -0.85 3.15 2.61 -0.61 0.00 0.59 -0.12 -1.69 0.14 0.98 0.00 4.23 -2.38 0.00 -0.51 0.00 0.87 0.87
2.24 0.00 0.53 1.51 1.51 -2.35 1.63 1.78 -0.94 0.00 0.87 -1.29 -0.95 1.36 0.00 3.28 2.29 1.16 2.64 0.88 0.00 -0.34 -1.65 0.00 -2.09 0.00 0.87 0.87
0.06 0.00 -3.83 -0.43 1.03 3.60 -1.14 -0.17 2.69 0.00 -0.69 5.14 4.17 -0.77 0.00 -0.97 0.49 -1.49 -1.20 -0.09 0.00 2.69 0.29 0.00 0.40 0.00 0.87 0.87
2.34 0.00 1.92 1.60 1.46 -1.97 4.07 -0.88 -0.35 0.00 0.60 -1.75 -1.10 1.54 0.00 1.77 -0.09 -0.35 4.65 3.47 0.00 0.36 -1.65 0.00 -2.19 0.00 0.87 0.87
3.56 0.00 -0.56 3.08 4.01 -2.96 3.46 0.68 -0.86 0.00 0.61 -1.47 -0.86 1.65 0.00 2.44 1.93 -0.41 1.83 1.56 0.00 0.12 -4.91 0.00 -2.67 0.00 0.87 0.87
1.59 0.00 -2.04 0.74 1.64 -0.20 0.62 0.32 -1.14 0.00 0.81 -0.20 -0.97 0.92 0.00 -0.07 0.56 1.53 2.23 0.21 0.00 -1.30 -0.69 0.00 0.04 0.00 0.87 0.87
1.76 0.00 -2.66 3.90 5.45 -3.07 2.38 1.83 1.09 0.00 1.32 0.56 0.65 1.73 0.00 1.13 4.50 0.18 0.20 0.84 0.00 2.14 -6.12 0.00 -2.99 0.00 4.55 4.55
0.57 0.00 -4.51 -0.66 0.05 2.08 -1.71 -0.46 2.21 0.00 3.59 4.32 4.87 -0.05 0.00 -0.45 1.01 0.88 -0.55 0.51 0.00 2.34 1.59 0.00 -0.98 0.00 4.55 4.55
4.31 0.00 2.80 1.03 1.03 -1.77 3.52 -1.31 1.53 0.00 0.57 -0.34 -0.04 1.04 0.00 2.50 -0.41 -0.72 5.34 3.75 0.00 2.41 -2.26 0.00 -2.19 0.00 4.55 4.55
4.74 0.00 -1.43 0.36 0.77 -0.38 0.92 -0.39 1.19 0.00 1.43 2.10 2.53 0.30 0.00 2.40 1.19 -0.39 1.01 1.53 0.00 2.06 -1.98 0.00 -1.81 0.00 4.55 4.55
3.51 0.00 1.23 0.46 0.46 0.06 1.08 0.82 4.18 0.00 -0.60 2.47 1.80 0.02 0.00 1.32 0.41 -1.03 0.19 1.45 0.00 5.05 -4.42 0.00 -0.32 0.00 4.55 4.55
0.79 0.00 -2.10 2.78 1.91 -1.99 0.99 0.86 1.55 0.00 2.21 0.69 1.51 1.02 0.00 0.79 1.57 1.55 0.42 1.92 0.00 2.12 -1.78 0.00 -2.33 0.00 4.55 4.55
2.32 0.00 -1.29 -0.01 -0.01 -1.03 0.59 -0.49 -1.33 0.00 3.70 -0.87 -0.58 1.35 0.00 0.73 0.30 3.20 4.44 0.86 0.00 -1.40 1.49 0.00 -1.00 0.00 4.55 4.55
5.00 0.00 0.17 0.46 0.82 -0.02 1.95 -0.97 1.80 0.00 0.01 1.97 1.98 0.43 0.00 1.70 0.09 -1.69 1.93 4.27 0.00 2.35 -2.37 0.00 -1.16 0.00 4.55 4.55
-2.55 0.00 -5.95 -2.39 -2.60 2.54 -3.01 0.83 -2.78 0.00 3.36 0.58 -1.46 2.63 0.00 -2.83 -0.44 6.18 2.03 -1.52 0.00 -3.89 5.08 0.00 3.02 0.00 4.55 4.55
3.64 0.00 0.44 2.21 1.97 -1.76 3.66 -0.75 3.33 0.00 -0.33 1.62 1.37 0.41 0.00 1.42 0.65 -1.71 1.00 1.89 0.00 5.44 -6.44 0.00 -2.04 0.00 4.55 4.55
1.26 0.00 -3.44 3.35 4.37 -4.35 1.02 1.47 -1.45 0.00 6.61 -2.18 0.11 2.59 0.00 2.55 3.18 3.52 1.71 1.58 0.00 -1.06 -2.90 0.00 -4.41 0.00 4.55 4.55
5.63 0.00 1.62 -0.17 0.07 -0.23 2.38 -1.35 3.78 0.00 -0.99 2.86 2.17 -0.53 0.00 1.71 -0.40 -2.30 0.92 1.85 0.00 5.48 -4.58 0.00 -0.57 0.00 4.55 4.55
3.69 0.00 0.50 3.58 2.62 -2.00 2.31 1.96 -0.88 0.00 0.61 -1.50 -1.43 4.77 0.00 0.16 1.47 -1.17 1.34 1.22 0.00 -0.72 -2.56 0.00 0.36 0.00 4.55 4.55
1.44 0.00 0.96 0.44 0.44 -0.70 1.15 -0.32 -0.13 0.00 0.26 -0.58 -0.39 0.51 0.00 0.83 -0.01 -0.05 2.20 0.64 0.00 -0.01 -0.10 0.00 -0.70 0.00 3.49 3.49
-0.31 0.00 -2.56 -1.23 -0.83 1.74 -0.42 -0.35 1.36 0.00 0.54 2.24 0.38 0.32 0.00 -0.98 -0.84 1.99 1.16 1.45 0.00 1.65 -0.65 0.00 1.18 0.00 4.55 4.55
3.32 0.00 1.76 2.69 2.62 -1.00 2.98 0.36 0.29 0.00 -0.22 -0.91 -0.93 1.69 0.00 0.48 0.47 -1.55 2.69 1.39 0.00 0.54 -2.57 0.00 -0.35 0.00 4.55 4.55
2.09 0.00 -2.78 4.65 6.06 -4.35 3.67 1.29 -1.59 0.00 4.02 -2.46 -0.75 2.97 0.00 1.87 3.18 1.45 2.15 1.80 0.00 -0.70 -5.12 0.00 -4.17 0.00 4.55 4.55
1.16 0.00 0.53 0.23 0.23 -0.12 0.96 0.90 4.01 0.00 0.54 2.53 2.04 0.05 0.00 1.13 0.19 -0.10 -0.16 2.71 0.00 5.58 -3.99 0.00 -0.72 0.00 4.55 4.55
3.66 0.00 1.79 3.71 3.18 -3.66 8.67 -0.41 -1.92 0.00 -0.21 -3.31 -2.18 2.83 0.00 2.25 1.31 -1.17 5.03 2.47 0.00 0.75 -5.01 0.00 -3.54 0.00 4.55 4.55
4.50 0.00 0.40 3.83 3.40 -4.36 7.52 -0.15 -1.59 0.00 0.27 -2.44 -1.29 2.59 0.00 2.36 3.12 -1.05 2.98 2.86 0.00 0.88 -6.11 0.00 -3.89 0.00 4.55 4.55
0.96 0.00 -1.81 4.77 4.96 -2.52 1.47 4.99 -0.03 0.00 0.98 -0.76 -0.97 2.73 0.00 1.00 3.31 0.97 -0.03 0.63 0.00 0.49 -4.86 0.00 -0.93 0.00 4.55 4.55
6.08 0.00 0.63 2.84 2.19 -2.71 2.52 0.01 1.70 0.00 0.60 -0.14 0.46 1.20 0.00 1.99 1.38 -0.68 1.74 2.05 0.00 1.91 -4.48 0.00 -2.05 0.00 4.55 4.55
0.64 0.00 -1.96 -1.22 -0.54 4.31 0.80 -1.52 4.27 0.00 -1.81 5.56 4.33 -1.14 0.00 -0.96 -0.78 -2.62 -0.34 0.60 0.00 4.56 -0.41 0.00 0.63 0.00 4.55 4.55


  [Part of this file has been deleted for brevity]

0.68 0.00 -0.46 3.83 2.79 -1.46 1.37 3.83 -1.48 0.00 1.16 -1.91 -2.02 6.82 0.00 -0.89 1.86 -0.16 0.74 0.55 0.00 -1.76 -1.09 0.00 1.29 0.00 4.55 4.55
-1.76 0.00 -1.47 -5.11 -3.02 7.73 -3.04 -0.48 3.60 0.00 -3.02 7.19 3.72 -2.84 0.00 -1.20 -3.38 -2.45 -1.41 -1.11 0.00 2.18 5.11 0.00 5.28 0.00 4.55 4.55
0.46 0.00 -3.38 2.90 3.62 -4.43 0.41 2.59 -1.76 0.00 5.62 -2.10 0.37 2.26 0.00 2.21 4.56 5.10 1.00 0.58 0.00 -1.45 -0.16 0.00 -4.33 0.00 4.55 4.55
-1.37 0.00 -1.85 -4.16 -2.80 8.65 -3.47 -0.72 4.79 0.00 -2.93 8.47 5.65 -2.59 0.00 -3.01 -2.44 -3.24 -2.58 -1.09 0.00 4.21 4.61 0.00 4.92 0.00 4.55 4.55
-0.92 0.00 -2.85 -3.67 -2.36 7.63 -3.04 -1.53 6.73 0.00 -2.36 9.07 6.57 -2.83 0.00 -2.18 -1.98 -2.83 -2.16 -0.37 0.00 5.88 2.31 0.00 2.95 0.00 4.55 4.55
2.50 0.00 1.34 2.36 2.18 -3.29 4.63 -0.88 -1.28 0.00 3.40 -2.89 -1.22 2.55 0.00 2.15 0.77 1.35 6.78 2.17 0.00 -0.38 -0.55 0.00 -3.65 0.00 4.55 4.55
1.02 0.00 -1.72 3.71 4.55 -2.08 1.58 4.50 -0.15 0.00 1.28 -0.72 -0.80 4.39 0.00 0.76 2.95 0.85 0.40 0.82 0.00 0.37 -4.04 0.00 -0.70 0.00 4.55 4.55
3.93 0.00 3.10 -1.45 -1.41 0.69 1.36 -1.22 3.44 0.00 -2.02 1.49 1.37 -1.29 0.00 1.02 -1.35 -2.31 1.39 1.47 0.00 4.57 -4.96 0.00 1.71 0.00 4.55 4.55
1.56 0.00 -2.33 -1.98 -1.19 5.27 -1.79 -1.53 6.20 0.00 -1.58 7.38 5.92 -1.92 0.00 -0.93 -0.74 -2.57 -1.25 0.54 0.00 5.64 -0.10 0.00 0.99 0.00 4.55 4.55
2.04 0.00 -1.15 -1.62 -1.07 3.84 -0.65 -1.64 6.31 0.00 -1.46 6.55 5.21 -1.80 0.00 -0.27 -0.80 -2.45 -0.89 0.89 0.00 6.71 -1.83 0.00 0.39 0.00 4.55 4.55
1.22 0.00 2.14 -0.07 -0.16 -0.32 1.17 0.93 2.98 0.00 0.15 0.88 0.71 0.11 0.00 1.22 -0.17 0.12 1.82 1.14 0.00 4.24 -3.30 0.00 0.14 0.00 4.55 4.55
1.74 0.00 1.45 -0.36 -0.36 0.61 1.35 -1.63 6.05 0.00 -0.36 3.35 2.72 -0.81 0.00 0.88 -1.31 -1.63 0.37 5.00 0.00 6.82 -4.87 0.00 -1.01 0.00 4.55 4.55
1.42 0.00 -3.76 -2.40 -1.34 6.13 -2.08 -1.38 5.20 0.00 -1.73 8.38 6.78 -2.06 0.00 -1.08 -0.46 -2.71 -1.68 0.11 0.00 5.21 1.32 0.00 1.27 0.00 4.55 4.55
6.12 0.00 0.01 3.88 3.23 -3.77 2.78 2.33 -0.81 0.00 1.45 -1.51 -0.83 2.52 0.00 2.43 2.67 0.03 1.66 1.81 0.00 -0.03 -4.64 0.00 -1.76 0.00 4.55 4.55
2.54 0.00 0.90 1.55 1.86 -1.97 2.03 1.15 0.76 0.00 1.32 -0.58 0.08 1.35 0.00 2.06 0.94 1.21 2.83 2.93 0.00 1.42 -1.60 0.00 -1.96 0.00 4.55 4.55
-0.44 0.00 -0.44 1.18 1.18 -0.72 -0.83 6.01 0.50 0.00 1.15 0.18 0.26 1.53 0.00 1.40 2.54 3.53 -0.83 -0.15 0.00 1.27 -0.07 0.00 0.13 0.00 4.55 4.55
0.82 0.00 -1.50 -2.02 -0.88 4.57 -1.52 1.23 3.02 0.00 -1.69 5.41 3.38 -0.96 0.00 -0.72 -0.66 -1.61 -1.21 -0.25 0.00 2.80 1.54 0.00 2.95 0.00 4.55 4.55
5.17 0.00 1.23 2.19 1.95 -4.22 5.46 0.10 -1.43 0.00 0.11 -2.40 -1.43 1.23 0.00 6.69 1.81 -0.05 3.39 2.55 0.00 1.10 -6.29 0.00 -4.67 0.00 4.55 4.55
4.19 0.00 -0.43 3.35 2.96 -4.08 5.31 0.07 -1.53 0.00 2.90 -2.53 -0.81 3.90 0.00 1.77 2.05 0.28 2.97 2.31 0.00 0.14 -4.14 0.00 -3.30 0.00 4.55 4.55
1.99 0.00 -3.87 9.25 7.73 -6.29 3.74 2.72 -1.45 0.00 2.91 -3.15 -2.17 4.05 0.00 0.73 4.23 0.49 1.45 1.45 0.00 -1.45 -7.25 0.00 -3.69 0.00 4.55 4.55
-1.21 0.00 -0.88 -5.63 -3.49 8.10 -3.04 -0.73 2.90 0.00 -3.14 6.59 2.49 -2.60 0.00 -3.05 -4.32 -2.26 -0.90 -1.45 0.00 0.84 6.29 0.00 7.23 0.00 4.55 4.55
3.45 0.00 1.70 2.54 2.27 -3.00 6.03 -1.06 -0.10 0.00 0.63 -2.00 -1.00 2.06 0.00 2.24 0.09 -1.15 3.73 7.15 0.00 1.27 -4.89 0.00 -3.06 0.00 4.55 4.55
3.63 0.00 0.32 0.13 0.96 -1.48 1.56 0.76 -0.13 0.00 -0.20 0.06 -0.26 -0.06 0.00 5.87 0.79 0.10 1.87 1.48 0.00 0.81 -3.39 0.00 -2.18 0.00 4.55 4.55
4.89 0.00 -1.70 5.71 6.41 -4.71 3.81 1.67 -1.03 0.00 1.37 -2.04 -1.31 2.70 0.00 2.79 3.25 -0.37 2.05 1.96 0.00 -0.34 -7.09 0.00 -3.47 0.00 4.55 4.55
2.59 0.00 -0.99 -0.55 -0.24 0.95 0.55 -1.22 4.26 0.00 0.89 4.17 3.90 -0.71 0.00 0.68 0.05 -0.90 -0.08 1.27 0.00 5.74 -2.63 0.00 -1.04 0.00 4.55 4.55
0.43 0.00 -3.37 2.50 2.70 -1.54 -0.18 5.16 -0.75 0.00 1.36 0.96 0.74 2.75 0.00 1.00 6.23 1.89 -1.08 -0.54 0.00 -0.42 -1.36 0.00 -0.97 0.00 4.55 4.55
6.97 0.00 1.05 1.63 1.75 -2.35 4.47 -1.19 0.29 0.00 0.24 0.21 1.34 1.15 0.00 2.37 1.01 -1.28 2.95 2.32 0.00 1.79 -4.77 0.00 -2.41 0.00 4.55 4.55
6.11 0.00 3.48 1.74 1.74 -2.76 4.35 -1.16 -0.43 0.00 0.87 -2.03 -1.30 1.89 0.00 3.19 0.15 -0.44 7.68 2.47 0.00 0.15 -1.03 0.00 -2.61 0.00 4.55 4.55
-1.24 0.00 -2.27 -3.72 -2.76 6.98 -3.57 -0.76 3.20 0.00 -1.11 7.29 6.27 -2.03 0.00 -3.11 -1.60 -0.58 -2.20 -1.12 0.00 2.66 3.14 0.00 3.74 0.00 4.55 4.55
1.53 0.00 -2.18 4.97 3.77 -3.67 2.06 2.19 0.68 0.00 1.79 -0.83 -0.49 3.86 0.00 0.68 4.09 0.41 0.73 1.71 0.00 0.34 -4.67 0.00 -2.33 0.00 4.55 4.55
0.39 0.00 -1.13 0.83 0.70 -2.97 -0.46 0.22 0.11 0.00 7.11 -2.15 0.66 1.56 0.00 0.54 1.17 3.70 1.79 1.45 0.00 -0.13 -1.33 0.00 -1.84 0.00 4.55 4.55
2.37 0.00 1.02 -2.12 -1.28 3.29 -0.07 -1.35 5.20 0.00 -1.89 4.81 2.92 -1.58 0.00 -0.33 -2.03 -2.60 -0.13 0.80 0.00 4.96 -1.19 0.00 2.09 0.00 4.55 4.55
-0.31 0.00 -2.90 -3.09 -2.12 6.97 -2.43 -1.32 5.92 0.00 -2.18 8.89 6.83 -2.54 0.00 -1.76 -1.21 -2.85 -2.36 -0.31 0.00 6.51 1.66 0.00 2.19 0.00 4.55 4.55
5.05 0.00 -0.67 2.76 3.42 -1.63 2.78 0.05 0.51 0.00 0.46 0.47 0.67 1.46 0.00 1.65 1.52 -1.22 2.76 1.73 0.00 1.06 -3.42 0.00 -1.92 0.00 4.55 4.55
1.58 0.00 -0.27 1.40 1.82 -1.02 3.17 -0.17 -0.12 0.00 1.04 -0.31 0.68 1.22 0.00 1.41 0.89 1.05 3.93 1.20 0.00 0.78 0.56 0.00 -2.58 0.00 4.55 4.55
0.53 0.00 0.93 -2.26 -1.56 3.27 0.40 -1.70 5.52 0.00 -1.56 5.25 3.41 -1.74 0.00 -0.13 -2.12 -2.00 0.88 0.68 0.00 6.52 -0.72 0.00 1.13 0.00 4.55 4.55
5.99 0.00 1.95 1.54 1.54 -3.21 3.07 -0.08 -0.64 0.00 1.57 -1.79 -0.35 1.52 0.00 3.13 1.10 1.24 4.80 1.98 0.00 0.10 -0.48 0.00 -2.82 0.00 4.55 4.55
0.82 0.00 0.45 1.16 0.98 -0.33 0.46 1.04 0.65 0.00 2.38 -0.48 -0.02 3.38 0.00 -0.39 0.12 0.15 0.88 3.55 0.00 0.14 -0.54 0.00 0.34 0.00 4.55 4.55
3.67 0.00 0.37 2.14 1.42 -1.78 2.48 -0.43 2.72 0.00 -0.12 1.29 1.07 0.40 0.00 1.32 0.67 -1.36 0.73 1.55 0.00 4.17 -5.19 0.00 -1.53 0.00 0.92 0.92
-0.39 0.00 -2.72 -2.37 -1.58 5.92 -2.57 -1.40 6.20 0.00 -1.58 7.51 5.92 -2.18 0.00 -1.58 -1.00 -2.18 -1.77 0.02 0.00 5.38 0.94 0.00 1.38 0.00 0.92 0.92
5.69 0.00 1.02 1.58 1.58 -2.62 2.72 -0.47 0.30 0.00 1.34 -0.72 0.12 1.31 0.00 2.31 0.68 -0.69 2.05 4.59 0.00 0.95 -3.79 0.00 -1.97 0.00 0.92 0.92
2.81 0.00 1.15 1.76 1.76 -1.90 1.70 2.20 -0.87 0.00 1.52 -1.53 -1.05 2.07 0.00 1.98 1.40 1.17 3.51 1.15 0.00 -0.59 -0.63 0.00 -1.10 0.00 0.92 0.92
0.18 0.00 -3.57 2.22 2.52 -3.57 -0.23 0.78 -1.19 0.00 8.20 -1.79 0.95 2.44 0.00 0.60 2.51 4.27 1.19 1.19 0.00 -1.19 -0.14 0.00 -3.51 0.00 0.92 0.92
-1.60 0.00 4.97 -2.92 -2.79 7.25 -3.39 1.42 0.90 0.00 -3.08 2.34 0.39 -0.72 0.00 -4.40 -3.21 -3.08 -2.32 -1.60 0.00 -0.17 5.69 0.00 7.95 0.00 0.92 0.92
-0.69 0.00 -1.86 1.52 1.46 -2.40 -0.89 4.21 -1.64 0.00 4.26 -1.88 -0.02 2.60 0.00 1.14 2.74 5.28 0.32 0.02 0.00 -1.64 2.53 0.00 -1.65 0.00 0.92 0.92
0.61 0.00 -1.16 2.35 2.76 -1.47 1.08 0.82 -0.41 0.00 0.61 -0.74 -0.53 1.08 0.00 0.20 1.23 0.00 0.41 0.41 0.00 -0.41 -2.25 0.00 -1.02 0.00 0.92 0.92
0.78 0.00 -0.96 -0.53 -0.24 1.41 -0.35 -0.35 1.14 0.00 -0.43 2.08 1.71 -0.45 0.00 -0.12 -0.02 -0.76 -0.33 0.10 0.00 1.27 0.22 0.00 0.24 0.00 0.92 0.92
1.78 0.00 0.47 1.04 0.90 -1.16 2.51 -0.35 -0.43 0.00 -0.14 -0.78 -0.43 0.69 0.00 0.74 0.41 -0.61 1.10 0.82 0.00 0.41 -1.92 0.00 -1.04 0.00 0.92 0.92
-0.43 0.00 1.43 -0.71 -0.71 1.86 -0.86 0.43 0.14 0.00 -0.86 0.43 -0.14 -0.14 0.00 -1.14 -0.86 -0.86 -0.57 -0.43 0.00 -0.14 1.57 0.00 2.14 0.00 0.92 0.92
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 0.00 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:

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
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

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