Biology – Quantitative Biology – Quantitative Methods
Scientific paper
2005-04-05
Lecture Notes in Computer Science 3907 (2006), 138-148
Biology
Quantitative Biology
Quantitative Methods
Scientific paper
10.1007/11732242_13
We introduce a new methodology for the determination of amino-acid substitution matrices for use in the alignment of proteins. The new methodology is based on a pre-existing set cover on the set of residues and on the undirected graph that describes residue exchangeability given the set cover. For fixed functional forms indicating how to obtain edge weights from the set cover and, after that, substitution-matrix elements from weighted distances on the graph, the resulting substitution matrix can be checked for performance against some known set of reference alignments and for given gap costs. Finding the appropriate functional forms and gap costs can then be formulated as an optimization problem that seeks to maximize the performance of the substitution matrix on the reference alignment set. We give computational results on the BAliBASE suite using a genetic algorithm for optimization. Our results indicate that it is possible to obtain substitution matrices whose performance is either comparable to or surpasses that of several others, depending on the particular scenario under consideration.
Barbosa Valmir C.
Porto A. H. L.
No associations
LandOfFree
A methodology for determining amino-acid substitution matrices from set covers does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with A methodology for determining amino-acid substitution matrices from set covers, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and A methodology for determining amino-acid substitution matrices from set covers will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-575866