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

Chris Fields cjfields at illinois.edu
Mon Jan 25 00:35:06 EST 2010


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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