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profit |
Function
Scan a sequence or database with a matrix or profileDescription
profit takes a simple frequency matrix produced by prophecy and searches with this to find matches in the input sequence(s) you are searching.Scores for the matches are calculated from the simple frequency matrix. It is the sum of scores at each position of the matrix.
A 'simple frequency matrix' is simply a count of the number of times any particular amino acid occurs at each position in the alignment used to create it. Simple frequency matrices are created using the program prophecy with the option '-type F' to create the correct type of matrix. The alignment should not have gaps in it.
The resulting matrix is moved to each position in the sequence(s) you are searching. At each position in the sequence, the frequencies of the amino acids or bases covered by the length of the matrix is read from the matrix. The sum of these frequencies at each position of the matrix is the score for that position of the sequence. If this 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 a sequence or database with a matrix or profile Profile or matrix file: outfile.prophecy Input sequence(s): tsw:* Output file [outfile.profit]: |
Go to the input files for this example
Go to the output files for this example
Command line arguments
Standard (Mandatory) qualifiers:
[-infile] infile Profile or matrix file
[-sequence] seqall Sequence database USA
[-outfile] outfile 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 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 deaths
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-infile] (Parameter 1) |
Profile or matrix file | Input file | Required |
| [-sequence] (Parameter 2) |
Sequence database USA | Readable sequence(s) | Required |
| [-outfile] (Parameter 3) |
Output file name | Output file | <sequence>.profit |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
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 sequence USAs.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 21 Percentage: 100 |
The ouput 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
None.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 | Creates matrices/profiles from multiple alignments |
| prophet | Gapped alignment for profiles |
Author(s)
Alan Bleasby (ajb © ebi.ac.uk)European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK