[Bioperl-l] Difference between (BLAST outputs)

T.D. Houfek 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"
characters differently.  

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
about this?


>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. 


 T.D. Hou
 Tobacco Genome Initiative
 NCSU, Raleigh, NC 27606

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