profit

## Wiki

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

## Function

Scan one or more sequences with a simple frequency matrix

## Description

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 prophecy

This 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' ```

## 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
(none)
(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
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
-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

### 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).

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.

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.

None.

## Exit status

It always exits with a status of 0.

## Known bugs

None.

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 Bleasby
European 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.

## History

Written (1999) - Alan Bleasby

## Target users

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