prophet.txt

emboss的linux版本的源代码

                                  prophet 



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


% prophet 
Gapped alignment for profiles
Input sequence(s): tsw:h*
Profile or weight matrix file: globins.gribskov
Gap opening coefficient [1.0]: 
Gap extension coefficient [1.0]: 
Output alignment [hd_fugru.prophet]: 

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

Command line arguments

   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

   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 standard output
   -filter             boolean    Read standard input, write 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

   prophet reads a GRIBSKOV or a HENIKOFF profile produced by prophecy
   and searches one or more sequence USAs.

  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       PIVDTGSVVSLSEEELSAVDKAWVKANSVAEVGGHALERGLFASEPMTLEFFDTFKYLSTFDL
SKGSADVKAHGKKVLDALGDAVAHLDDLEGTLAALSDLHAHKLKKGVDPVNFKLLSHCLLVVLASHLPGDFTPEVQASM
DKFLASVATVLASKYRELGYQG
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 0.0
0 -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 0.0
0 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 0.0
0 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 0.0
0 -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.
26 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 0.3
0 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.
18 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 0.0
0 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.
39 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.
00 -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 0.0
0 -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 0.2
6 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 0.0
0 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.
46 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 0.0
0 -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.
00 -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.
00 -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.
00 -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.
47 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 0.0
0 -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