
                               contactalign 



Function

   EMBOSS implementation of Damian Counsell's 2.5-D alignment algorithm

Description

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

Algorithm

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

Usage

   Under development, no final example yet

Command line arguments

   Standard (Mandatory) qualifiers:
  [-querysequence]     sequence   First (query) polypeptide sequence to be
                                  aligned
  [-templatesequence]  sequence   Second (template) polypeptide sequence to be
                                  aligned
   -gapopen            float      The gap opening penalty is subtracted from
                                  the total score every time a gap is inserted
                                  in the alignment. The default value is
                                  chosen for the EBLOSUM62 scoring matrix when
                                  you are aligning protein sequences, and the
                                  EDNAFULL matrix when you are aligning
                                  nucleotide sequences. If you sequence
                                  contains many small errors you should set a
                                  low gap opening penalty (near zero) to avoid
                                  over-penalizing those errors.
   -gapextend          float      The gap extension penalty is the score
                                  substracted when more spaces are added to an
                                  existing alignment gap. Often a single
                                  insertion or deletion affects multiple
                                  residues/nucleotides; separate opening and
                                  extension penalties reduce the excessive
                                  penalty such events would otherwise carry;
                                  generally the gap extension penalty should
                                  be significantly lower than the gap opening
                                  penalty.
  [-alignedoutfile]    seqout     Output sequence USA

   Additional (Optional) qualifiers:
   -substitutionscoringfile matrixf    Matrix of scores for specific amino acid
                                  residue type substitution within
                                  one-dimensional sequence strings
   -contactscoringfile matrixf    Matrix of scores for frequency of contacts
                                  between specific amino acid residue types

   Advanced (Unprompted) qualifiers:
   -[no]zeroend        boolean    If this option is true then no penalty is
                                  added for gaps at either ends of a trace.

   Associated qualifiers:

   "-querysequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the 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

   "-templatesequence" associated qualifiers
   -sbegin2            integer    Start of the sequence to be used
   -send2              integer    End of the 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

   "-alignedoutfile" associated qualifiers
   -osformat3          string     Output seq format
   -osextension3       string     File name extension
   -osname3            string     Base file name
   -osdirectory3       string     Output directory
   -osdbname3          string     Database name to add
   -ossingle3          boolean    Separate file for each entry
   -oufo3              string     UFO features
   -offormat3          string     Features format
   -ofname3            string     Features file name
   -ofdirectory3       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
   [-querysequence]
   (Parameter 1) First (query) polypeptide sequence to be aligned
   Readable sequence Required
   [-templatesequence]
   (Parameter 2) Second (template) polypeptide sequence to be aligned
   Readable sequence Required
   -gapopen The gap opening penalty is subtracted from the total score
   every time a gap is inserted in the alignment. The default value is
   chosen for the EBLOSUM62 scoring matrix when you are aligning protein
   sequences, and the EDNAFULL matrix when you are aligning nucleotide
   sequences. If you sequence contains many small errors you should set a
   low gap opening penalty (near zero) to avoid over-penalizing those
   errors. Floating point number from 1.0 to 100.0 10.0 for any sequence
   -gapextend The gap extension penalty is the score substracted when
   more spaces are added to an existing alignment gap. Often a single
   insertion or deletion affects multiple residues/nucleotides; separate
   opening and extension penalties reduce the excessive penalty such
   events would otherwise carry; generally the gap extension penalty
   should be significantly lower than the gap opening penalty. Floating
   point number from 0.0 to 10.0 0.5 for any sequence
   [-alignedoutfile]
   (Parameter 3) Output sequence USA Writeable sequence <sequence>.format
   Additional (Optional) qualifiers Allowed values Default
   -substitutionscoringfile Matrix of scores for specific amino acid
   residue type substitution within one-dimensional sequence strings
   Comparison matrix file in EMBOSS data path EBLOSUM62 for protein
   EDNAFULL for DNA
   -contactscoringfile Matrix of scores for frequency of contacts between
   specific amino acid residue types Comparison matrix file in EMBOSS
   data path EBLOSUM62 for protein
   EDNAFULL for DNA
   Advanced (Unprompted) qualifiers Allowed values Default
   -[no]zeroend If this option is true then no penalty is added for gaps
   at either ends of a trace. Boolean value Yes/No Yes

Input file format

   contactalign reads any normal sequence USAs.

   Under development, no example input file(s) yet

Output file format

   contactalign 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 Runs alignment program on all sequence pairs in a
   directory
   esim4 Align an mRNA to a genomic DNA sequence
   est2genome Align EST and genomic DNA sequences
   nawalign Damian Counsell's implementation for protein sequences of the
   Needleman and Wunsch alignment algorithm
   nawalignrunner Runs nawalign alignment program on all sequence pairs
   in a directory
   needle Needleman-Wunsch global alignment
   needlerunner Runs needle alignment program on all sequence pairs in a
   directory
   scorer Scores accuracy of protein-protein sequence alignment against
   gold standard structure-structure alignment
   scorerrunner Runs scorer to compare ordered pairs of substituted seqs
   in two directories and write the scores to a third
   stretcher Finds the best global alignment between two sequences
   substitute Substitutes matches from first (query) sequence of two
   aligned sequences in a trace into second (template sequence)
   substituterunner Runs substitute on directory of traces and writes
   substituted sequences to another

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
