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prophet |
Wiki
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Function
Scan one or more sequences with a Gribskov or Henikoff profileDescription
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
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) |
seqall | Sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| [-infile] (Parameter 2) |
infile | Profile or weight matrix file | Input file | Required |
| -gapopen | float | Gap opening coefficient | Number from 0.000 to 100.000 | 1.0 |
| -gapextend | float | Gap extension coefficient | Number from 0.000 to 100.000 | 1.0 |
| [-outfile] (Parameter 3) |
align | Output alignment file name | (default -aformat simple) | <*>.prophet |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-sequence" associated seqall 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 |
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
| -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 align qualifiers | ||||
| -aformat3 -aformat_outfile |
string | Alignment format | Any string | simple |
| -aextension3 -aextension_outfile |
string | File name extension | Any string | |
| -adirectory3 -adirectory_outfile |
string | Output directory | Any string | |
| -aname3 -aname_outfile |
string | Base file name | Any string | |
| -awidth3 -awidth_outfile |
integer | Alignment width | Any integer value | 0 |
| -aaccshow3 -aaccshow_outfile |
boolean | Show accession number in the header | Boolean value Yes/No | N |
| -adesshow3 -adesshow_outfile |
boolean | Show description in the header | Boolean value Yes/No | N |
| -ausashow3 -ausashow_outfile |
boolean | Show the full USA in the alignment | Boolean value Yes/No | N |
| -aglobal3 -aglobal_outfile |
boolean | Show the full sequence in alignment | Boolean value Yes/No | N |
| 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
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 PIVDTGSVVSLSEEELSAVDKAWVKANSVAEVGGHALERGLFASEPMTLEFFDTFKYLSTFDLSKGSADVKAHGKKVLDALGDAVAHLDDLEGTLAALSDLHAHKLKKGVDPVNFKLLSHCLLVVLASHLPGDFTPEVQASMDKFLASVATVLASKYRELGYQG 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 0.26 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 0.30 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 0.18 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 0.00 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 0.39 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 0.00 -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 0.46 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 0.00 -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 0.00 -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 0.00 -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 0.55 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 0.38 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 0.00 -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 0.00 -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 BleasbyEuropean 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.