As the research of disordered proteins progresses and more disordered protein sequences are discovered, an optimal substitution matrix for the alignment of these sequences must be elucidated. The currently used substitution matrices, PAM and BLOSUM, are ideal for the alignment of general protein sequences. But it is discovered that this set of matrices is not adequate for the specific alignment of disordered protein sequences. By implementing genetic algorithms, a substitution matrix improved for the alignment of disordered proteins has been achieved. The genetic algorithm determined matrix performed two times better when compared to BLOSUM62 and PAM250.
Library of Congress Subject Headings
Proteins--Structure--Mathematical models; Genetic algorithms
Kim, Dong, "Determining a substitution matrix for the alignment of disordered proteins" (2013). Thesis. Rochester Institute of Technology. Accessed from
RIT – Main Campus