
                                  profit 



Function

   Scan a sequence or database with a matrix or profile

Description

   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 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 a sequence or database with a matrix or profile
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 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 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

   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

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
