
                                substitute 



Function

   Substitutes matches from first (query) sequence of two aligned
   sequences in a trace into second (template sequence)

Description

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

Algorithm

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

Usage

   Under development, no final example yet

Command line arguments

   Standard (Mandatory) qualifiers:
  [-alignedpairsequence] seqset     Pair of polypeptide sequences to be
                                  substituted
  [-substitutedoutseq] seqout     Output sequence USA

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

   "-alignedpairsequence" 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

   "-substitutedoutseq" associated qualifiers
   -osformat2          string     Output seq format
   -osextension2       string     File name extension
   -osname2            string     Base file name
   -osdirectory2       string     Output directory
   -osdbname2          string     Database name to add
   -ossingle2          boolean    Separate file for each entry
   -oufo2              string     UFO features
   -offormat2          string     Features format
   -ofname2            string     Features file name
   -ofdirectory2       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
   [-alignedpairsequence]
   (Parameter 1) Pair of polypeptide sequences to be substituted Readable
   set of sequences Required
   [-substitutedoutseq]
   (Parameter 2) Output sequence USA Writeable sequence <sequence>.format
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

Input file format

   substitute reads any normal sequence USAs.

   Under development, no example input file(s) yet

Output file format

   substitute 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
   contactalign EMBOSS implementation of Damian Counsell's 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 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
   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
