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What is meaning of Biased???

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What is meaning of Biased???

Postby bioinfo » Thu Sep 30, 2010 9:35 am

The probability values in a PSSM depend on the number of sequences used to
compile the matrix. Because the matrix is often constructed from the alignment of an
insufficient number of closely related sequences, to increase the predictive power of
the model, a weighting scheme similar to the one used in the Clustal algorithm is used that downweights overrepresented, closely related sequences and
upweights underrepresented and divergent ones, so that more divergent sequences
can be included.

Application of such a weighting scheme makes the matrix less biased
and able to detect more distantly related sequences.

I want meaning of this last sentence.I am confused about the meaning of Biased in Bioinformatics topics..

Kindly help..Awaiting for reply.
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Postby canalon » Thu Sep 30, 2010 1:55 pm

Biased as in statistical bias: Your sample do not represent the entire population since the sampling cannot/do not take entirely random element within the population. In this case the sequences available are not representative of the true diversity because most of them come from very closely related organisms. I do not know what your field is, but if you look at microbiology, any sequence coverage is likely to include lots of enterobacteria (they are easy to grow, they have been studied for a very long time, and they are clinically relevant) and much less of the rest. But that weight is not representative of their real presence in the biosphere.
Patrick

Science has proof without any certainty. Creationists have certainty without
any proof. (Ashley Montague)
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