substitute

 

Function

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

Description

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Algorithm

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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

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Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
alignrunnerRuns alignment program on all sequence pairs in a directory
contactalignEMBOSS implementation of Damian Counsell's 2.5-D alignment algorithm
esim4Align an mRNA to a genomic DNA sequence
est2genomeAlign EST and genomic DNA sequences
nawalignDamian Counsell's implementation for protein sequences of the Needleman and Wunsch alignment algorithm
nawalignrunnerRuns nawalign alignment program on all sequence pairs in a directory
needleNeedleman-Wunsch global alignment
needlerunnerRuns needle alignment program on all sequence pairs in a directory
scorerScores accuracy of protein-protein sequence alignment against gold standard structure-structure alignment
scorerrunnerRuns scorer to compare ordered pairs of substituted seqs in two directories and write the scores to a third
stretcherFinds the best global alignment between two sequences
substituterunnerRuns 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