
                                  profit 



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]: 

   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 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. 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

   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 22 Percentage: 100
HBB_PANPA 22 Percentage: 100
HBB_PANTR 22 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

   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 Bleasby (ajb © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

History

   Written (1999) - Alan Bleasby

Target users

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

Comments

   None
