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Alphabets and Alignments

Des Higgins dazzhiggins at hotmail.com
Sun Mar 20 18:36:10 EST 2005

"Dr Engelbert Buxbaum" <engelbert_buxbaum at hotmail.com> wrote in message 
news:d09481$hvj$01$1 at news.t-online.com...
> 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

Paper by Marin van Heel

 A new family of powerful multivariate statistical sequence analysis 
J Mol Biol. 1991 Aug 20;220(4):877-87.
PMID: 1880802 [PubMed - indexed for MEDLINE]

> 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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