[Bioperl-l] Distance between non-overlapping sequences in DNAStatistics
Jason Stajich
jason at bioperl.org
Mon Jan 25 05:58:03 UTC 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/
http://twitter.com/hyphaltip
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