
                               needlerunner 



Function

   Runs needle alignment program on all sequence pairs in a directory

Description

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

Algorithm

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

Usage

   Under development, no final example yet

Command line arguments

   Standard (Mandatory) qualifiers:
  [-seqpairsdir]       dirlist    Input directory of files containing sequence
                                  pairs for alignment
  [-pathtocommand]     directory  Directory where alignment executable lives
  [-commandname]       string     Name of alignment executable
  [-scoringmatrixdirname] directory  Directory where scoring matrix lives
  [-scoringmatrixname] string     Name of alignment scoring matrix
   -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.
  [-alignedseqsoutdir] outdir     Name of directory containing sequences
                                  aligned by needle
  [-outfilesuffix]     string     Appended to end of all output alignment file
                                  names
  [-outfileformat]     string     Format of output alignments

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


   Error: File /homes/pmr/local/share/EMBOSS/acd/needlerunner.acd line
   12: (seqpairsdir) Unknown attribute 'name'

Input file format

   needlerunner reads any normal sequence USAs.

   Under development, no example input file(s) yet

Output file format

   needlerunner 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
   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
