[Bioperl-l] Difference between (BLAST outputs)
tdhoufek at unity.ncsu.edu
Fri Jan 30 16:23:05 EST 2004
It looks to me as if the different implementations are handling "N"
The first appears to be reckoning as a mismatch any pairing of N with a
known nucleotide. The second, at least to my mind, makes
a strange assumption: namely, that because an "N" *might* in fact be a
"T", that we may safely assume that is the case.
In this case, given the general level of identity, match is probably a
better guess than mismatch. Still seems strange. Does anyone know more
>Maybe someone could help me out with this problem, I've tried to >
>email ncbi about this but they didn't bother answering. Basically,
>I'm seeing a difference in the data being output by stand-alone >
>blast and online blast.
Tobacco Genome Initiative
NCSU, Raleigh, NC 27606
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