                                   prophet



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Scan one or more sequences with a Gribskov or Henikoff profile

Description

   prophet scans one or more sequences with the supplied Gribskov or
   Henikoff profile (produced by prophecy). It writes the the
   highest-scoring (gapped) alignment for each sequence to file, which
   includes the score for the match. Gap opening coefficient and gap
   extension coefficient must be specified.

Algorithm

   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


% prophet
Scan one or more sequences with a Gribskov or Henikoff profile
Input sequence(s): tsw:h*
Profile or weight matrix file: globins.gribskov
Gap opening coefficient [1.0]:
Gap extension coefficient [1.0]:
Output alignment [hba_human.prophet]:


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

Command line arguments

Scan one or more sequences with a Gribskov or Henikoff profile
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
  [-infile]            infile     Profile or weight matrix file
   -gapopen            float      [1.0] Gap opening coefficient (Number from
                                  0.000 to 100.000)
   -gapextend          float      [1.0] Gap extension coefficient (Number from
                                  0.000 to 100.000)
  [-outfile]           align      [*.prophet] Output alignment file name
                                  (default -aformat simple)

   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
   -aformat3           string     Alignment format
   -aextension3        string     File name extension
   -adirectory3        string     Output directory
   -aname3             string     Base file name
   -awidth3            integer    Alignment width
   -aaccshow3          boolean    Show accession number in the header
   -adesshow3          boolean    Show description in the header
   -ausashow3          boolean    Show the full USA in the alignment
   -aglobal3           boolean    Show the full sequence in alignment

   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


Input file format

   prophet reads one or more nucleotide or protein sequences.

   The input is a standard EMBOSS sequence query (also known as a 'USA').

   Major sequence database sources defined as standard in EMBOSS
   installations include srs:embl, srs:uniprot and ensembl

   Data can also be read from sequence output in any supported format
   written by an EMBOSS or third-party application.

   The input format can be specified by using the command-line qualifier
   -sformat xxx, where 'xxx' is replaced by the name of the required
   format. The available format names are: gff (gff3), gff2, embl (em),
   genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
   dasgff and debug.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats. prophet also reads a GRIBSKOV or a
   HENIKOFF profile produced by prophecy.

  Input files for usage example

   'tsw:h*' is a sequence entry in the example protein database 'tsw'

  File: globins.gribskov

# 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       645.45
Threshold       75
Gap_open        3.00
Gap_extend      0.30
Consensus       PIVDTGSVVSLSEEELSAVDKAWVKANSVAEVGGHALERGLFASEPMTLEFFDTFKYLSTFDLS
KGSADVKAHGKKVLDALGDAVAHLDDLEGTLAALSDLHAHKLKKGVDPVNFKLLSHCLLVVLASHLPGDFTPEVQASMDK
FLASVATVLASKYRELGYQG
0.15 0.00 0.03 0.03 0.03 -0.18 0.09 0.06 -0.06 0.00 0.03 -0.09 -0.06 0.00 0.00 0
.45 0.09 0.09 0.12 0.09 0.00 0.03 -0.24 0.00 -0.24 0.00 0.87 0.87
0.00 0.00 0.06 -0.06 -0.06 0.18 -0.09 -0.09 0.45 0.00 -0.06 0.24 0.18 -0.09 0.00
 -0.06 -0.09 -0.09 -0.03 0.06 0.00 0.33 -0.15 0.00 0.03 0.00 0.87 0.87
0.06 0.00 0.06 -0.06 -0.06 0.06 0.06 -0.09 0.33 0.00 -0.06 0.24 0.18 -0.09 0.00
0.03 -0.06 -0.09 -0.03 0.06 0.00 0.45 -0.24 0.00 -0.03 0.00 0.87 0.87
0.09 0.00 -0.15 0.45 0.30 -0.30 0.18 0.12 -0.06 0.00 0.09 -0.15 -0.12 0.18 0.00
0.03 0.18 0.00 0.06 0.06 0.00 -0.06 -0.33 0.00 -0.15 0.00 0.87 0.87
0.12 0.00 0.06 0.06 0.06 -0.09 0.12 -0.03 0.06 0.00 0.06 -0.03 0.00 0.06 0.00 0.
09 -0.03 -0.03 0.09 0.45 0.00 0.06 -0.18 0.00 -0.09 0.00 0.87 0.87
0.18 0.00 0.06 0.18 0.15 -0.18 0.45 -0.06 -0.09 0.00 -0.03 -0.15 -0.09 0.12 0.00
 0.09 0.06 -0.09 0.18 0.12 0.00 0.06 -0.30 0.00 -0.18 0.00 0.87 0.87
0.12 0.00 0.18 0.06 0.06 -0.09 0.18 -0.06 -0.03 0.00 0.06 -0.12 -0.09 0.09 0.00
0.12 -0.03 0.03 0.45 0.09 0.00 -0.03 0.09 0.00 -0.12 0.00 0.87 0.87
0.13 0.00 0.13 -0.13 -0.13 0.13 0.13 -0.19 0.69 0.00 -0.13 0.50 0.38 -0.19 0.00
0.06 -0.13 -0.19 -0.06 0.13 0.00 0.94 -0.50 0.00 -0.06 0.00 0.87 0.87
0.59 0.00 -0.06 -0.07 -0.02 0.24 0.31 -0.25 0.68 0.00 -0.20 0.72 0.60 -0.14 0.00
 0.14 -0.03 -0.39 0.03 0.23 0.00 0.97 -0.55 0.00 -0.12 0.00 0.87 0.87
0.52 0.00 0.12 0.35 0.35 -0.54 0.38 0.41 -0.22 0.00 0.20 -0.30 -0.22 0.31 0.00 0
.76 0.53 0.27 0.61 0.20 0.00 -0.08 -0.38 0.00 -0.48 0.00 0.87 0.87
0.01 0.00 -0.88 -0.10 0.24 0.83 -0.26 -0.04 0.62 0.00 -0.16 1.19 0.96 -0.18 0.00
 -0.22 0.11 -0.34 -0.28 -0.02 0.00 0.62 0.07 0.00 0.09 0.00 0.87 0.87
0.54 0.00 0.44 0.37 0.34 -0.45 0.94 -0.20 -0.08 0.00 0.14 -0.40 -0.25 0.35 0.00
0.41 -0.02 -0.08 1.07 0.80 0.00 0.08 -0.38 0.00 -0.51 0.00 0.87 0.87
0.82 0.00 -0.13 0.71 0.92 -0.68 0.80 0.16 -0.20 0.00 0.14 -0.34 -0.20 0.38 0.00
0.56 0.45 -0.09 0.42 0.36 0.00 0.03 -1.13 0.00 -0.61 0.00 0.87 0.87
0.37 0.00 -0.47 0.17 0.38 -0.05 0.14 0.07 -0.26 0.00 0.19 -0.05 -0.22 0.21 0.00
-0.01 0.13 0.35 0.52 0.05 0.00 -0.30 -0.16 0.00 0.01 0.00 0.87 0.87
0.41 0.00 -0.61 0.90 1.26 -0.71 0.55 0.42 0.25 0.00 0.31 0.13 0.15 0.40 0.00 0.2
6 1.04 0.04 0.05 0.19 0.00 0.49 -1.41 0.00 -0.69 0.00 4.55 4.55
0.13 0.00 -1.04 -0.15 0.01 0.48 -0.39 -0.11 0.51 0.00 0.83 0.99 1.12 -0.01 0.00
-0.10 0.23 0.20 -0.13 0.12 0.00 0.54 0.36 0.00 -0.23 0.00 4.55 4.55
1.00 0.00 0.64 0.24 0.24 -0.41 0.81 -0.30 0.35 0.00 0.13 -0.08 -0.01 0.24 0.00 0
.58 -0.09 -0.17 1.23 0.86 0.00 0.56 -0.52 0.00 -0.50 0.00 4.55 4.55
1.09 0.00 -0.33 0.08 0.18 -0.09 0.21 -0.09 0.27 0.00 0.33 0.48 0.58 0.07 0.00 0.
55 0.27 -0.09 0.23 0.35 0.00 0.48 -0.45 0.00 -0.42 0.00 4.55 4.55
0.81 0.00 0.28 0.11 0.11 0.02 0.25 0.19 0.96 0.00 -0.14 0.57 0.42 0.00 0.00 0.30
 0.09 -0.24 0.04 0.33 0.00 1.16 -1.02 0.00 -0.07 0.00 4.55 4.55
0.18 0.00 -0.48 0.64 0.44 -0.46 0.23 0.20 0.36 0.00 0.51 0.16 0.35 0.23 0.00 0.1
8 0.36 0.36 0.10 0.44 0.00 0.49 -0.41 0.00 -0.54 0.00 4.55 4.55
0.54 0.00 -0.30 0.00 0.00 -0.24 0.14 -0.11 -0.31 0.00 0.85 -0.20 -0.13 0.31 0.00
 0.17 0.07 0.74 1.03 0.20 0.00 -0.32 0.34 0.00 -0.23 0.00 4.55 4.55
1.15 0.00 0.04 0.11 0.19 -0.01 0.45 -0.22 0.41 0.00 0.00 0.45 0.45 0.10 0.00 0.3
9 0.02 -0.39 0.45 0.98 0.00 0.54 -0.54 0.00 -0.27 0.00 4.55 4.55
-0.59 0.00 -1.37 -0.55 -0.60 0.59 -0.70 0.19 -0.64 0.00 0.77 0.14 -0.34 0.60 0.0
0 -0.65 -0.10 1.43 0.47 -0.35 0.00 -0.90 1.17 0.00 0.70 0.00 4.55 4.55
0.84 0.00 0.10 0.51 0.46 -0.41 0.84 -0.17 0.76 0.00 -0.08 0.37 0.31 0.10 0.00 0.
33 0.15 -0.39 0.23 0.43 0.00 1.25 -1.48 0.00 -0.47 0.00 4.55 4.55
0.29 0.00 -0.79 0.77 1.01 -1.00 0.24 0.34 -0.33 0.00 1.52 -0.50 0.03 0.60 0.00 0
.59 0.73 0.81 0.39 0.36 0.00 -0.24 -0.67 0.00 -1.02 0.00 4.55 4.55
1.29 0.00 0.37 -0.04 0.02 -0.05 0.55 -0.31 0.87 0.00 -0.23 0.66 0.50 -0.12 0.00
0.39 -0.09 -0.53 0.21 0.43 0.00 1.26 -1.05 0.00 -0.13 0.00 4.55 4.55
0.85 0.00 0.11 0.82 0.60 -0.46 0.53 0.45 -0.20 0.00 0.14 -0.35 -0.33 1.10 0.00 0
.04 0.34 -0.27 0.31 0.28 0.00 -0.17 -0.59 0.00 0.08 0.00 4.55 4.55
0.33 0.00 0.22 0.10 0.10 -0.16 0.27 -0.07 -0.03 0.00 0.06 -0.13 -0.09 0.12 0.00
0.19 0.00 -0.01 0.51 0.15 0.00 0.00 -0.02 0.00 -0.16 0.00 3.49 3.49
-0.07 0.00 -0.59 -0.28 -0.19 0.40 -0.10 -0.08 0.31 0.00 0.12 0.51 0.09 0.08 0.00
 -0.22 -0.19 0.46 0.27 0.34 0.00 0.38 -0.15 0.00 0.27 0.00 4.55 4.55
0.76 0.00 0.40 0.62 0.60 -0.23 0.69 0.08 0.07 0.00 -0.05 -0.21 -0.21 0.39 0.00 0
.11 0.11 -0.36 0.62 0.32 0.00 0.13 -0.59 0.00 -0.08 0.00 4.55 4.55
0.48 0.00 -0.64 1.07 1.40 -1.00 0.84 0.30 -0.37 0.00 0.92 -0.57 -0.17 0.68 0.00
0.43 0.73 0.33 0.49 0.41 0.00 -0.16 -1.18 0.00 -0.96 0.00 4.55 4.55
0.27 0.00 0.12 0.05 0.05 -0.03 0.22 0.21 0.92 0.00 0.13 0.58 0.47 0.01 0.00 0.26
 0.04 -0.02 -0.04 0.63 0.00 1.28 -0.92 0.00 -0.17 0.00 4.55 4.55
0.84 0.00 0.41 0.85 0.73 -0.84 1.99 -0.09 -0.44 0.00 -0.05 -0.76 -0.50 0.65 0.00
 0.52 0.30 -0.27 1.16 0.57 0.00 0.17 -1.15 0.00 -0.81 0.00 4.55 4.55
1.04 0.00 0.09 0.88 0.78 -1.00 1.73 -0.04 -0.37 0.00 0.06 -0.56 -0.30 0.60 0.00
0.54 0.72 -0.24 0.69 0.66 0.00 0.20 -1.41 0.00 -0.90 0.00 4.55 4.55
0.22 0.00 -0.42 1.10 1.14 -0.58 0.34 1.15 -0.01 0.00 0.23 -0.17 -0.22 0.63 0.00
0.23 0.76 0.22 -0.01 0.15 0.00 0.11 -1.12 0.00 -0.21 0.00 4.55 4.55
1.40 0.00 0.14 0.65 0.50 -0.62 0.58 0.00 0.39 0.00 0.14 -0.03 0.11 0.28 0.00 0.4
6 0.32 -0.15 0.40 0.47 0.00 0.44 -1.03 0.00 -0.47 0.00 4.55 4.55
0.15 0.00 -0.45 -0.28 -0.13 0.99 0.18 -0.35 0.98 0.00 -0.42 1.28 1.00 -0.26 0.00
 -0.22 -0.18 -0.60 -0.08 0.14 0.00 1.05 -0.09 0.00 0.15 0.00 4.55 4.55


  [Part of this file has been deleted for brevity]

0.16 0.00 -0.11 0.88 0.64 -0.34 0.31 0.88 -0.34 0.00 0.27 -0.44 -0.47 1.57 0.00
-0.20 0.43 -0.04 0.17 0.13 0.00 -0.41 -0.25 0.00 0.30 0.00 4.55 4.55
-0.40 0.00 -0.34 -1.18 -0.69 1.78 -0.70 -0.11 0.83 0.00 -0.69 1.65 0.86 -0.65 0.
00 -0.27 -0.78 -0.56 -0.32 -0.26 0.00 0.50 1.18 0.00 1.21 0.00 4.55 4.55
0.11 0.00 -0.78 0.67 0.83 -1.02 0.09 0.60 -0.41 0.00 1.29 -0.48 0.09 0.52 0.00 0
.51 1.05 1.17 0.23 0.13 0.00 -0.33 -0.04 0.00 -1.00 0.00 4.55 4.55
-0.32 0.00 -0.42 -0.96 -0.65 1.99 -0.80 -0.17 1.10 0.00 -0.68 1.95 1.30 -0.60 0.
00 -0.69 -0.56 -0.75 -0.59 -0.25 0.00 0.97 1.06 0.00 1.13 0.00 4.55 4.55
-0.21 0.00 -0.66 -0.84 -0.54 1.76 -0.70 -0.35 1.55 0.00 -0.54 2.09 1.51 -0.65 0.
00 -0.50 -0.46 -0.65 -0.50 -0.09 0.00 1.36 0.53 0.00 0.68 0.00 4.55 4.55
0.57 0.00 0.31 0.54 0.50 -0.76 1.07 -0.20 -0.29 0.00 0.79 -0.67 -0.28 0.59 0.00
0.49 0.18 0.31 1.56 0.50 0.00 -0.09 -0.13 0.00 -0.84 0.00 4.55 4.55
0.24 0.00 -0.40 0.85 1.05 -0.48 0.36 1.03 -0.03 0.00 0.30 -0.16 -0.18 1.01 0.00
0.17 0.68 0.19 0.09 0.19 0.00 0.09 -0.93 0.00 -0.16 0.00 4.55 4.55
0.91 0.00 0.71 -0.33 -0.32 0.16 0.31 -0.28 0.79 0.00 -0.46 0.35 0.32 -0.30 0.00
0.24 -0.31 -0.53 0.32 0.34 0.00 1.05 -1.14 0.00 0.39 0.00 4.55 4.55
0.36 0.00 -0.54 -0.45 -0.27 1.21 -0.41 -0.35 1.43 0.00 -0.36 1.70 1.36 -0.44 0.0
0 -0.21 -0.17 -0.59 -0.29 0.12 0.00 1.30 -0.03 0.00 0.23 0.00 4.55 4.55
0.47 0.00 -0.26 -0.37 -0.25 0.88 -0.15 -0.38 1.45 0.00 -0.34 1.51 1.20 -0.41 0.0
0 -0.06 -0.18 -0.56 -0.21 0.21 0.00 1.55 -0.42 0.00 0.09 0.00 4.55 4.55
0.28 0.00 0.49 -0.02 -0.04 -0.07 0.27 0.21 0.69 0.00 0.04 0.21 0.17 0.02 0.00 0.
28 -0.04 0.03 0.42 0.26 0.00 0.98 -0.76 0.00 0.03 0.00 4.55 4.55
0.40 0.00 0.33 -0.08 -0.08 0.14 0.31 -0.38 1.39 0.00 -0.08 0.77 0.63 -0.19 0.00
0.20 -0.30 -0.38 0.08 1.15 0.00 1.57 -1.12 0.00 -0.23 0.00 4.55 4.55
0.33 0.00 -0.86 -0.55 -0.31 1.41 -0.48 -0.32 1.20 0.00 -0.40 1.93 1.56 -0.47 0.0
0 -0.25 -0.11 -0.62 -0.39 0.03 0.00 1.20 0.30 0.00 0.29 0.00 4.55 4.55
1.41 0.00 0.00 0.89 0.74 -0.87 0.64 0.54 -0.19 0.00 0.34 -0.35 -0.19 0.58 0.00 0
.56 0.61 0.01 0.38 0.42 0.00 -0.01 -1.07 0.00 -0.41 0.00 4.55 4.55
0.59 0.00 0.21 0.36 0.43 -0.45 0.47 0.27 0.17 0.00 0.31 -0.13 0.02 0.31 0.00 0.4
7 0.22 0.28 0.65 0.68 0.00 0.32 -0.37 0.00 -0.45 0.00 4.55 4.55
-0.10 0.00 -0.10 0.27 0.27 -0.17 -0.19 1.38 0.12 0.00 0.26 0.04 0.06 0.35 0.00 0
.32 0.58 0.81 -0.19 -0.03 0.00 0.30 -0.02 0.00 0.03 0.00 4.55 4.55
0.19 0.00 -0.34 -0.46 -0.20 1.05 -0.35 0.28 0.70 0.00 -0.39 1.24 0.78 -0.22 0.00
 -0.16 -0.15 -0.37 -0.28 -0.06 0.00 0.65 0.35 0.00 0.68 0.00 4.55 4.55
1.19 0.00 0.28 0.51 0.45 -0.97 1.26 0.02 -0.33 0.00 0.03 -0.55 -0.33 0.28 0.00 1
.54 0.42 -0.01 0.78 0.59 0.00 0.25 -1.45 0.00 -1.08 0.00 4.55 4.55
0.97 0.00 -0.10 0.77 0.68 -0.94 1.22 0.02 -0.35 0.00 0.67 -0.58 -0.19 0.90 0.00
0.41 0.47 0.06 0.68 0.53 0.00 0.03 -0.95 0.00 -0.76 0.00 4.55 4.55
0.46 0.00 -0.89 2.13 1.78 -1.45 0.86 0.63 -0.33 0.00 0.67 -0.72 -0.50 0.93 0.00
0.17 0.97 0.11 0.33 0.33 0.00 -0.33 -1.67 0.00 -0.85 0.00 4.55 4.55
-0.28 0.00 -0.20 -1.30 -0.80 1.86 -0.70 -0.17 0.67 0.00 -0.72 1.52 0.57 -0.60 0.
00 -0.70 -0.99 -0.52 -0.21 -0.33 0.00 0.19 1.45 0.00 1.66 0.00 4.55 4.55
0.79 0.00 0.39 0.59 0.52 -0.69 1.39 -0.24 -0.02 0.00 0.15 -0.46 -0.23 0.47 0.00
0.52 0.02 -0.26 0.86 1.64 0.00 0.29 -1.13 0.00 -0.70 0.00 4.55 4.55
0.84 0.00 0.07 0.03 0.22 -0.34 0.36 0.17 -0.03 0.00 -0.05 0.01 -0.06 -0.01 0.00
1.35 0.18 0.02 0.43 0.34 0.00 0.19 -0.78 0.00 -0.50 0.00 4.55 4.55
1.12 0.00 -0.39 1.32 1.48 -1.09 0.88 0.39 -0.24 0.00 0.32 -0.47 -0.30 0.62 0.00
0.64 0.75 -0.09 0.47 0.45 0.00 -0.08 -1.63 0.00 -0.80 0.00 4.55 4.55
0.59 0.00 -0.23 -0.13 -0.06 0.22 0.13 -0.28 0.98 0.00 0.21 0.96 0.90 -0.16 0.00
0.16 0.01 -0.21 -0.02 0.29 0.00 1.32 -0.60 0.00 -0.24 0.00 4.55 4.55
0.10 0.00 -0.78 0.58 0.62 -0.35 -0.04 1.19 -0.17 0.00 0.31 0.22 0.17 0.63 0.00 0
.23 1.43 0.43 -0.25 -0.12 0.00 -0.10 -0.31 0.00 -0.22 0.00 4.55 4.55
1.60 0.00 0.24 0.38 0.40 -0.54 1.03 -0.27 0.07 0.00 0.06 0.05 0.31 0.26 0.00 0.5
5 0.23 -0.29 0.68 0.53 0.00 0.41 -1.10 0.00 -0.55 0.00 4.55 4.55
1.41 0.00 0.80 0.40 0.40 -0.64 1.00 -0.27 -0.10 0.00 0.20 -0.47 -0.30 0.43 0.00
0.74 0.03 -0.10 1.77 0.57 0.00 0.03 -0.24 0.00 -0.60 0.00 4.55 4.55
-0.29 0.00 -0.52 -0.86 -0.64 1.61 -0.82 -0.18 0.74 0.00 -0.25 1.68 1.44 -0.47 0.
00 -0.72 -0.37 -0.13 -0.51 -0.26 0.00 0.61 0.72 0.00 0.86 0.00 4.55 4.55
0.35 0.00 -0.50 1.14 0.87 -0.84 0.47 0.50 0.16 0.00 0.41 -0.19 -0.11 0.89 0.00 0
.16 0.94 0.09 0.17 0.40 0.00 0.08 -1.08 0.00 -0.54 0.00 4.55 4.55
0.09 0.00 -0.26 0.19 0.16 -0.68 -0.11 0.05 0.03 0.00 1.63 -0.49 0.15 0.36 0.00 0
.12 0.27 0.85 0.41 0.33 0.00 -0.03 -0.31 0.00 -0.42 0.00 4.55 4.55
0.55 0.00 0.24 -0.49 -0.29 0.76 -0.02 -0.31 1.20 0.00 -0.43 1.11 0.67 -0.36 0.00
 -0.07 -0.47 -0.60 -0.03 0.19 0.00 1.14 -0.28 0.00 0.48 0.00 4.55 4.55
-0.07 0.00 -0.67 -0.71 -0.49 1.61 -0.56 -0.30 1.36 0.00 -0.50 2.05 1.57 -0.58 0.
00 -0.41 -0.28 -0.66 -0.54 -0.07 0.00 1.50 0.38 0.00 0.51 0.00 4.55 4.55
1.16 0.00 -0.16 0.64 0.79 -0.38 0.64 0.01 0.12 0.00 0.11 0.11 0.16 0.34 0.00 0.3
8 0.35 -0.28 0.63 0.40 0.00 0.24 -0.79 0.00 -0.44 0.00 4.55 4.55
0.36 0.00 -0.06 0.32 0.42 -0.24 0.73 -0.04 -0.03 0.00 0.24 -0.07 0.16 0.28 0.00
0.32 0.21 0.24 0.90 0.28 0.00 0.18 0.13 0.00 -0.60 0.00 4.55 4.55
0.12 0.00 0.21 -0.52 -0.36 0.75 0.09 -0.39 1.27 0.00 -0.36 1.21 0.79 -0.40 0.00
-0.03 -0.49 -0.46 0.20 0.16 0.00 1.50 -0.16 0.00 0.26 0.00 4.55 4.55
1.38 0.00 0.45 0.35 0.35 -0.74 0.71 -0.02 -0.15 0.00 0.36 -0.41 -0.08 0.35 0.00
0.72 0.25 0.28 1.10 0.46 0.00 0.02 -0.11 0.00 -0.65 0.00 4.55 4.55
0.19 0.00 0.10 0.27 0.22 -0.07 0.10 0.24 0.15 0.00 0.55 -0.11 0.00 0.78 0.00 -0.
09 0.03 0.03 0.20 0.82 0.00 0.03 -0.12 0.00 0.08 0.00 4.55 4.55
0.85 0.00 0.09 0.49 0.33 -0.41 0.57 -0.10 0.63 0.00 -0.03 0.30 0.25 0.09 0.00 0.
30 0.15 -0.31 0.17 0.36 0.00 0.96 -1.20 0.00 -0.35 0.00 0.92 0.92
-0.09 0.00 -0.63 -0.54 -0.36 1.36 -0.59 -0.32 1.43 0.00 -0.36 1.73 1.36 -0.50 0.
00 -0.36 -0.23 -0.50 -0.41 0.00 0.00 1.24 0.21 0.00 0.32 0.00 0.92 0.92
1.31 0.00 0.23 0.36 0.36 -0.60 0.63 -0.11 0.07 0.00 0.31 -0.17 0.03 0.30 0.00 0.
53 0.16 -0.16 0.47 1.05 0.00 0.22 -0.87 0.00 -0.45 0.00 0.92 0.92
0.65 0.00 0.26 0.40 0.40 -0.44 0.39 0.51 -0.20 0.00 0.35 -0.35 -0.24 0.48 0.00 0
.46 0.32 0.27 0.81 0.26 0.00 -0.14 -0.14 0.00 -0.25 0.00 0.92 0.92
0.04 0.00 -0.82 0.51 0.58 -0.82 -0.05 0.18 -0.27 0.00 1.89 -0.41 0.22 0.56 0.00
0.14 0.58 0.98 0.27 0.27 0.00 -0.27 -0.03 0.00 -0.81 0.00 0.92 0.92
-0.37 0.00 1.14 -0.67 -0.64 1.67 -0.78 0.33 0.21 0.00 -0.71 0.54 0.09 -0.17 0.00
 -1.01 -0.74 -0.71 -0.53 -0.37 0.00 -0.04 1.31 0.00 1.83 0.00 0.92 0.92
-0.16 0.00 -0.43 0.35 0.34 -0.55 -0.20 0.97 -0.38 0.00 0.98 -0.43 0.00 0.60 0.00
 0.26 0.63 1.21 0.07 0.00 0.00 -0.38 0.58 0.00 -0.38 0.00 0.92 0.92
0.14 0.00 -0.27 0.54 0.64 -0.34 0.25 0.19 -0.09 0.00 0.14 -0.17 -0.12 0.25 0.00
0.05 0.28 0.00 0.09 0.09 0.00 -0.09 -0.52 0.00 -0.24 0.00 0.92 0.92
0.18 0.00 -0.22 -0.12 -0.06 0.32 -0.08 -0.08 0.26 0.00 -0.10 0.48 0.39 -0.10 0.0
0 -0.03 0.00 -0.17 -0.07 0.02 0.00 0.29 0.05 0.00 0.06 0.00 0.92 0.92
0.41 0.00 0.11 0.24 0.21 -0.27 0.58 -0.08 -0.10 0.00 -0.03 -0.18 -0.10 0.16 0.00
 0.17 0.09 -0.14 0.25 0.19 0.00 0.09 -0.44 0.00 -0.24 0.00 0.92 0.92
-0.10 0.00 0.33 -0.16 -0.16 0.43 -0.20 0.10 0.03 0.00 -0.20 0.10 -0.03 -0.03 0.0
0 -0.26 -0.20 -0.20 -0.13 -0.10 0.00 -0.03 0.36 0.00 0.49 0.00 0.92 0.92
0.07 0.00 -0.20 0.20 0.20 -0.26 0.07 0.20 -0.10 0.00 0.13 -0.03 0.00 0.13 0.00 0
.10 0.49 0.13 -0.03 -0.03 0.00 -0.07 -0.16 0.00 -0.20 0.00 0.92 0.92
0.20 0.00 0.07 0.20 0.16 -0.20 0.49 -0.07 -0.10 0.00 -0.03 -0.16 -0.10 0.13 0.00
 0.10 0.07 -0.10 0.20 0.13 0.00 0.07 -0.33 0.00 -0.20 0.00 0.92 0.92

Output file format

   The output is a standard EMBOSS alignment file.

   The results can be output in one of several styles by using the
   command-line qualifier -aformat xxx, where 'xxx' is replaced by the
   name of the required format. Some of the alignment formats can cope
   with an unlimited number of sequences, while others are only for pairs
   of sequences.

   The available multiple alignment format names are: multiple, simple,
   fasta, msf, clustal, mega, meganon, nexus,, nexusnon, phylip,
   phylipnon, selex, treecon, tcoffee, debug, srs.

   The available pairwise alignment format names are: pair, markx0,
   markx1, markx2, markx3, markx10, match, sam, bam, score, srspair

   See: http://emboss.sf.net/docs/themes/AlignFormats.html for further
   information on alignment formats.

   By default the output is in 'simple' format.

  Output files for usage example

  File: hba_human.prophet

########################################
# Program: prophet
# Rundate: Fri 15 Jul 2011 12:00:00
# Commandline: prophet
#    -sequence "tsw:h*"
#    -infile ../../data/globins.gribskov
# Align_format: simple
# Report_file: hba_human.prophet
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: globins
# 2: HBA_HUMAN
# Matrix: EBLOSUM62
#
# Length: 144
# Identity:      94/144 (65.3%)
# Similarity:   104/144 (72.2%)
# Gaps:           3/144 ( 2.1%)
# Score: 161.14
#
#
#=======================================

globins           15 ELSAVDKAWVKANSVAEVGGHALERGLFASEPMTLEFFDTFKYLSTFDLS     64
                     .||..||..|||.. .:||.||.|.|..|.|.|.|.|..|..|...||||
HBA_HUMAN          2 VLSPADKTNVKAAW-GKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLS     50

globins           65 KGSADVKAHGKKVLDALGDAVAHLDDLEGTLAALSDLHAHKLKKGVDPVN    114
                     .|||.||.|||||.|||.:||||:||:...|:||||||||||:  |||||
HBA_HUMAN         51 HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLR--VDPVN     98

globins          115 FKLLSHCLLVVLASHLPGDFTPEVQASMDKFLASVATVLASKYR    158
                     ||||||||||.||:|||.:|||.|.||:|||||||:|||.||||
HBA_HUMAN         99 FKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR    142


#=======================================
#
# Aligned_sequences: 2
# 1: globins
# 2: HBA_PANPA
# Matrix: EBLOSUM62
#
# Length: 144
# Identity:      94/144 (65.3%)
# Similarity:   104/144 (72.2%)
# Gaps:           3/144 ( 2.1%)


  [Part of this file has been deleted for brevity]

                     :....| ..|| .|..:.........:.:......:....|...|....:
HD_TAKRU        2289 LQQPCVWNKLSTPEYNTHTCSLIYCLHHIILAVAVSPGDQLLHPERKKTK   2338

globins           51 FFDTFKYLSTFDLSKGSADVKAHGKKVLDALGDAVAHLDDLEGT-LAALS     99
                     ...........|....:..::....:::..|.:.:..:..|... ..|..
HD_TAKRU        2339 ALRHSDDEDQVDSVHDNHTLEWQACEIMAELVEGLQSVLSLGHHRNTAFP   2388

globins          100 DLHAHKLKKGVDPVNFKLLSHCLLVVLASHLPGDFTPEVQASMDKFLASV    149
                     ......|:..:..::...|.:....|........::|:........|..:
HD_TAKRU        2389 AFLTPTLRNIIISLSRLPLVNSHTRVPPLVWKLGWSPQPGGEFGTTLPEI   2438

globins          150 ATV-LASK--YRELGYQ    163
                     ... |..|  :||..|:
HD_TAKRU        2439 PVDFLQEKDVFREFLYR   2455


#=======================================
#
# Aligned_sequences: 2
# 1: globins
# 2: HIRA_TAKRU
# Matrix: EBLOSUM62
#
# Length: 161
# Identity:       8/161 ( 5.0%)
# Similarity:    40/161 (24.8%)
# Gaps:           2/161 ( 1.2%)
# Score: 64.35
#
#
#=======================================

globins            1 PIVDTGSVVSLSEE-ELSAVDKAWVKANSVAEVGGHALERGLFASEPMTL     49
                     ......|...|:.. .............|..:....:.::....::.:..
HIRA_TAKRU       574 ATAAIASSTGLTPSERPKESTPMQKDVKSKEDTSSDSEDKMATINKNLAF    623

globins           50 EFFDTFKYLSTFDLSKGSADVKAHGKKVLDALGDAVAHLDDLEGTLAALS     99
                     ........:...::.:.....:....|:..::...:...........:.:
HIRA_TAKRU       624 NKRKPELLMDGAEVVEKRKKGRPRKDKMAASIAQPLTQTTSPAEREPSRA    673

globins          100 DLHAHKLKKGVDPVNFKLLSHCLLVVLASHLPGDFTPEVQASMDKFLASV    149
                     ................||.:..:.......:..|.:..::...:..:.:.
HIRA_TAKRU       674 AAAGAGAAAPTAAAALKLPTPSIKKAFTLQVSMDPSVVLEVENEVSVVAG    723

globins          150 ATVLASKY-RE    159
                     :.:...:. |:
HIRA_TAKRU       724 SRLSQLRCSRD    734


#---------------------------------------
#---------------------------------------

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 exits with a status of 0.

Known bugs

   None.

See also

                    Program name                         Description
                    profit       Scan one or more sequences with a simple frequency matrix
                    prophecy     Create frequency matrix or profile from a multiple alignment

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 (c) emboss.open-bio.org) not to the original author.

History

                    Written (1999) - Alan Bleasby

Target users

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

Comments

                    None
