[Biojava-l] API for global alignments

[Richard Holland]

1.4 doesn't have anything for this, but 1.5 will do (the code is already
in the head branch of CVS). Needleman-Wunsch and Smith-Waterman
implementations are both in the org.biojava.bio.alignment package.

cheers,
Richard

On Wed, 2006-07-05 at 10:51 +0930, Michael Tran wrote:
> Hi
>  
> Looking for an API/class for doing global alignments (like a clustalW alignment) given a FASTA file.
>  
> The BioJava API 1.4 doesn't seem to have this.
>  
> org.biojava.bio.alignment <https://webmail.acpfg.local/org/biojava/bio/alignment/package-summary.html>  
> Interfaces  
> AlignmentElement <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/AlignmentElement.html>  
> ARAlignment <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/ARAlignment.html>  
> EditableAlignment <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/EditableAlignment.html>  
> QualitativeAlignment <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/QualitativeAlignment.html>  
> UnequalLengthAlignment <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/UnequalLengthAlignment.html> 	
> Classes  
> AbstractULAlignment <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/AbstractULAlignment.html>  
> FlexibleAlignment <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/FlexibleAlignment.html>  
> SimpleAlignmentElement <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/SimpleAlignmentElement.html> 	
> Exceptions  
> IllegalAlignmentEditException <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/IllegalAlignmentEditException.html> 	
> 
> Any help appreciated.
> 
> Cheers,
> 
> MT
> 
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-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416