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Alphabets and Alignments

Dr Engelbert Buxbaum engelbert_buxbaum at hotmail.com
Thu Mar 10 23:25:36 EST 2005

bioinformatically at gmail.com wrote:

> I'm not a bioinformatician but, I was wondering ... many sequence
> alignments make comparisons at the amino-acid level because this
> technique is more sensitive than using nucleotide bases. Right? What
> are the problems, other than heuristic, concerned with increasing the
> alphabet again wrt amino-acid 'environments' --- say, doublets or
> triplets? Would the resulting information have improved utility in
> structural or evolutionary analyses?

There was a paper on this in the J.Mol.Biol. in the early 90's (sorry,
don't recall the exact reference). The idea was to put the frequency of
all aa triplets into a 3-d matrix, then do a matrix reduction and use
the result to calculate the homology of proteins (avoiding the
computationally expensive multi-sequence alignment).

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