[Bioperl-l] Distance between non-overlapping sequences in DNAStatistics

Jason Stajich jason at bioperl.org
Mon Jan 25 00:58:03 EST 2010


It could also return -1 which is used as place holder for NA in other  
programs that generate distance matrices.
-jason
On Jan 24, 2010, at 9:35 PM, Chris Fields wrote:

> Just a quick question for those using DNAStatistics.  I just fixed a  
> bug in Bio::Align::DNAStatistics that failed with a div by zero  
> error (bug 2901) on this data:
>
>> seq1
> GGTACCAGCAGGTGGGCCGCCTACTGCGCACGCGCGGGTTTGCGGGCAGCCGC
>> seq2
> GGTACCAGCTGGTGGGCCGCCTACTGCGCACGCGCGGGTTTGCGGGCAGCCGC
>> seq3
> GGTACCAGCAGGTGGTCCGCCTA------------------------------
>> seq4
> --------------------------CGCACGCGCGTGTTTGCGGGCAGCCGC
>
> Since seq3 and seq4 don't overlap, the distance can't be  
> calculated.  In our case, I replace the score with 'NA' as a  
> placeholder, but I'm worried about downstream app breakage.  Anyone  
> have an objection to using 'NA' here, or know of ways this may lead  
> to problems elsewhere?
>
> chris
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--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org
http://fungalgenomes.org/
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