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LION
2009
Springer
114views Optimization» more  LION 2009»
13 years 11 months ago
Substitution Matrices and Mutual Information Approaches to Modeling Evolution
Abstract. Substitution matrices are at the heart of Bioinformatics: sequence alignment, database search, phylogenetic inference, protein family classication are based on Blosum, P...
Stephan Kitchovitch, Yuedong Song, Richard C. van ...
WICSA
2008
13 years 6 months ago
Analyzing the Evolution of Large-Scale Software Systems Using Design Structure Matrices and Design Rule Theory: Two Exploratory
Software modularization activities remain without the guidance of formal theories and models. According to Baldwin and Clark's [1] design rule theory (DRT) , modular architec...
Matthew J. LaMantia, Yuanfang Cai, Alan MacCormack...
BMCBI
2008
130views more  BMCBI 2008»
13 years 4 months ago
A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins
Background: The most common substitution matrices currently used (BLOSUM and PAM) are based on protein sequences with average amino acid distributions, thus they do not represent ...
Kevin Brick, Elisabetta Pizzi
BMCBI
2004
126views more  BMCBI 2004»
13 years 4 months ago
A probabilistic model for the evolution of RNA structure
Background: For the purposes of finding and aligning noncoding RNA gene- and cis-regulatory elements in multiple-genome datasets, it is useful to be able to derive multi-sequence ...
Ian Holmes
BIOSYSTEMS
2008
129views more  BIOSYSTEMS 2008»
13 years 4 months ago
Reconstruction of DNA sequences using genetic algorithms and cellular automata: Towards mutation prediction?
Change of DNA sequence that fuels evolution is, to a certain extent, a deterministic process because mutagenesis does not occur in an absolutely random manner. So far, it has not ...
Ch. Mizas, Georgios Ch. Sirakoulis, Vasilios A. Ma...