Tehdyt toimenpiteet
|
profit |
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 simple frequency matrixDescription
profit scans one or more sequences with a simple frequency matrix and writes an output file with any high-scoring matches. All possible ungapped alignments of each sequence to the matrix are scored and any matches with a score higher than the specified threshold are written to the output file. The output file includes the name of any matching sequence found, the start position in the sequence of the match and the percentage of the maximum possible score.
Algorithm
All possible ungapped alignments of each sequence to the frequency matrix are scored. The first alignment has the first positions of the sequence and matrix in the same register. If the sequence is larger than the matrix, there will be more than one alignment. Otherwise, there will be just one.
The score for a match is simply the sum of scores at each position of the matrix for the corresponding residue from the sequence. The percentage of the maximum possible score reported in the output file is the sum of the highest value at each position in the frequency matrix. Where the match score is above the threshold percentage of the maximum possible score for that matrix, then a hit is reported.
Usage
Before running the example, we need to make a simple frequency matrix using prophecyThis is the ungapped aligned set of sequences used to make the matrix:
% more m.seq >one DEVGGEALGRLLVVYPWTQR >two DEVGREALGRLLVVYPWTQR >three DEVGGEALGRILVVYPWTQR >four DEVGGEAAGRVLVVYPWTQR% prophecy Creates matrices/profiles from multiple alignments Input sequence set: m.seq Profile type F : Frequency G : Gribskov H : Henikoff Select type [F]: Enter a name for the profile [mymatrix]: Enter threshold reporting percentage [75]: Output file [outfile.prophecy]:
Here is a sample session with profit
% profit Scan one or more sequences with a simple frequency matrix Profile or weight matrix file: outfile.prophecy Input sequence(s): tsw:* Output file [outfile.profit]: ajSeqxrefNewDbS '1-I' 'FT025' |
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 simple frequency matrix
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-infile] infile Profile or weight matrix file
[-sequence] seqall Sequence(s) filename and optional format, or
reference (input USA)
[-outfile] outfile [*.profit] Output file name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin2 integer Start of each sequence to be used
-send2 integer End of each sequence to be used
-sreverse2 boolean Reverse (if DNA)
-sask2 boolean Ask for begin/end/reverse
-snucleotide2 boolean Sequence is nucleotide
-sprotein2 boolean Sequence is protein
-slower2 boolean Make lower case
-supper2 boolean Make upper case
-sformat2 string Input sequence format
-sdbname2 string Database name
-sid2 string Entryname
-ufo2 string UFO features
-fformat2 string Features format
-fopenfile2 string Features file name
"-outfile" associated qualifiers
-odirectory3 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 | ||||
| [-infile] (Parameter 1) |
infile | Profile or weight matrix file | Input file | Required |
| [-sequence] (Parameter 2) |
seqall | Sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| [-outfile] (Parameter 3) |
outfile | Output file name | Output file | <*>.profit |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-sequence" associated seqall qualifiers | ||||
| -sbegin2 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 |
| -send2 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 |
| -sreverse2 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask2 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide2 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein2 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower2 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper2 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
| -sformat2 -sformat_sequence |
string | Input sequence format | Any string | |
| -sdbname2 -sdbname_sequence |
string | Database name | Any string | |
| -sid2 -sid_sequence |
string | Entryname | Any string | |
| -ufo2 -ufo_sequence |
string | UFO features | Any string | |
| -fformat2 -fformat_sequence |
string | Features format | Any string | |
| -fopenfile2 -fopenfile_sequence |
string | Features file name | Any string | |
| "-outfile" associated outfile qualifiers | ||||
| -odirectory3 -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
profit reads a simple frequency matrix produced by prophecy and uses it to search searches one or more protein or nucleic acid 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.
Input files for usage example
'tsw:*' is a sequence entry in the example protein database 'tsw'
File: outfile.prophecy
# Pure Frequency Matrix # Columns are amino acid counts A->Z # Rows are alignment positions 1->n Simple Name mymatrix Length 20 Maximum score 76 Thresh 75 Consensus DEVGGEALGRLLVVYPWTQR 0 0 0 4 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 4 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 4 0 0 0 0 0 0 0 0 0 0 0 4 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 3 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 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 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 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 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 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 4 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 4 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 4 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 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 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 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 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 4 0 0 0 0 0 0 0 0 0 |
Output file format
Output files for usage example
File: outfile.profit
# PROF scan using simple frequency matrix mymatrix # Scores >= threshold 75 (max score 76) # HBB_HUMAN 22 Percentage: 100 HBB_PANPA 22 Percentage: 100 HBB_PANTR 22 Percentage: 100 |
The output is a list of three columns.
The first column is the name of the matching sequence found.
The second is the start position in the sequence of the match.
The third column (after the word 'Percentage:') is the percentage of the
maximum possible score (sum of the highest value at each
position in the frequency matrix).
Data files
None.Notes
A 'simple frequency matrix' is simply a table containing a count of the number of times any particular amino acid occurs at each position in the sequence alignment from which it was derived. Simple frequency matrices are created using the program prophecy with the option -type F to create the correct type of matrix. The input alignment should not have gaps in it.
References
None.Warnings
The aligned set of sequences used to make the simple frquency matrix should not have gaps in it. profit will let you use a matrix made from a gapped alignment, but the results will probably not be sensible.Diagnostic Error Messages
None.Exit status
It always exits with a status of 0.Known bugs
None.See also
| Program name | Description |
|---|---|
| prophecy | Create frequency matrix or profile from a multiple alignment |
| prophet | Scan one or more sequences with a Gribskov or Henikoff profile |
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.