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 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' 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 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 Bleasby European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) 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. Comments None