nawalign

 

Function

Damian Counsell's NW implementation

Description

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

Algorithm

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

Usage

Under development, no final example yet

Command line arguments

   Standard (Mandatory) qualifiers:
  [-across]            sequence   First (query) polypeptide sequence to be
                                  aligned
  [-down]              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
  [-verticaltrace]     outfile    Output file name

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

   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:

   "-across" 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

   "-down" 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

   "-verticaltrace" associated qualifiers
   -odirectory4        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
[-across]
(Parameter 1)
First (query) polypeptide sequence to be aligned Readable sequence Required
[-down]
(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
[-verticaltrace]
(Parameter 4)
Output file name Output file <sequence>.nawalign
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
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

nawalign reads any normal sequence USAs.

Under development, no example input file(s) yet

Output file format

nawalign 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 nameDescription
alignrunnerAlign sequence pairs in a directory
comparatorCompare contact scores of two sequence alignments
contactalignDamian Counsell's experimental 2.5-D alignment algorithm
esim4Align an mRNA to a genomic DNA sequence
est2genomeAlign EST and genomic DNA sequences
nawalignrunnerNawalign all sequence pairs in a directory
needleNeedleman-Wunsch global alignment
needlerunnerNeedle all sequence pairs in a directory
scorerScore alignments using structural alignments
scorerrunnerSCORER for ordered pairs of substituted seqs
stretcherFinds the best global alignment between two sequences
substituteSubstitute matches into a template
substituterunnerRun 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