
                                comparator 



Function

   Compare contact scores of two sequence alignments

Description

   **************** EDIT HERE ****************

Algorithm

   **************** EDIT HERE ****************

Usage

   Under development, no final example yet

Command line arguments

   Standard (Mandatory) qualifiers:
  [-goldpairseqset]    seqset     pair of gold standard aligned aa sequences
                                  to be substituted
  [-testpairseqset]    seqset     pair of aligned aa sequences to be
                                  substituted
  [-contactscoringfile] matrixf    Matrix of scores for frequency of contacts
                                  between specific amino acid residue types
  [-cmaptemplate]      infile     contact map of template structure
  [-scoringtrace]      outfile    scored vertical trace of template sequence
                                  against both alignments

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-goldpairseqset" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-testpairseqset" 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

   "-scoringtrace" associated qualifiers
   -odirectory5        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
   [-goldpairseqset]
   (Parameter 1) pair of gold standard aligned aa sequences to be
   substituted Readable set of sequences contacttest/1hgxa0_1hmpa0.ali
   [-testpairseqset]
   (Parameter 2) pair of aligned aa sequences to be substituted Readable
   set of sequences contacttest/1hgx_a_1hmp_a.fasta
   [-contactscoringfile]
   (Parameter 3) Matrix of scores for frequency of contacts between
   specific amino acid residue types Comparison matrix file in EMBOSS
   data path contactscores.dat
   [-cmaptemplate]
   (Parameter 4) contact map of template structure Input file 1hgx_a.con
   [-scoringtrace]
   (Parameter 5) scored vertical trace of template sequence against both
   alignments Output file scored.trace
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   comparator reads any normal sequence USAs.

   Under development, no example input file(s) yet

Output file format

   comparator outputs a graph to the specified graphics device. outputs a
   report format file. The default format is ...

   Under development, no example output file(s) yet

Data files

   **************** EDIT HERE ****************

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

     Program name                         Description
   alignrunner      Align sequence pairs in a directory
   contactalign     Damian Counsell's experimental 2.5-D alignment algorithm
   esim4            Align an mRNA to a genomic DNA sequence
   est2genome       Align EST and genomic DNA sequences
   nawalign         Damian Counsell's NW implementation
   nawalignrunner   Nawalign all sequence pairs in a directory
   needle           Needleman-Wunsch global alignment
   needlerunner     Needle all sequence pairs in a directory
   scorer           Score alignments using structural alignments
   scorerrunner     SCORER for ordered pairs of substituted seqs
   stretcher        Finds the best global alignment between two sequences
   substitute       Substitute matches into a template
   substituterunner Run SUBSTITUTE on a directory of traces

Author(s)

   Damian Counsell (d.counsell © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

Target users

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

Comments

   None
