[Biojava-l] BioJava 2 status

[Andreas Prlic]

For an example that uses the blosum 62 matrix
see the junit test org.biojava.bio.align.SubstitutionMatrixTest

Andreas





On 17 Sep 2007, at 11:09, Richard Holland wrote:

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> @see org.biojava.bio.align.SubstitutionMatrix
>
> Basically it doesn't include any matrices, but the above class will  
> load
> matrix definition files the user has downloaded from the NCBI FTP  
> site,
> so you can obtain standard matrices that way.
>
>
> Matthew Pocock wrote:
>> Somebody asked me:
>>
>>> I was wondering whether BioJava provides standard scoring matrices
>>> (e.g. BLOSUM62, etc.) as "constants" anywhere for doing  
>>> alignments. I
>>> couldn't seem to find this anywhere in the code but, admittedly,  
>>> have
>>> not looked very closely yet.
>>
>> And rather embarasingly, I don't know the answer. Does someone here?
>>
>> Matthew
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>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
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Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
			 +44 (0) 1223 49 6891

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