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This program determines the optimal alignment of two nucleotide sequences using the Smith–Waterman algorithm. Optimality, of course, is determined by the values of the gap penalty g and the weight matrix (that lists all of the s(ai , bj )). Finally the program outputs the optimal similarity score along with the optimal alignment.
Implementation of Smith-Waterman local alignment model- find closest local alignments in two given amino acid sequences. BLOSUM was used as the scoring matrix.
MSc Biology C++ Course Assignment. A program that can either perform a global, or local sequence alignment. Implementation of the Smith-Waterman and Needleman-Wunsch algorithms.
I developed a R package implementing the Smith-Waterman algorithm. The package building, check and installation works smoothly with 0 error (see log_file). BiocCheck results show 1 error because I’m not registered at the support site, 1 warning because BiocViews terms are invalid. Check the log_file for more details.
An R script that calculates a similarity matrix for a list of protein sequences with the aid of Bleakley-Yamanishi Normalized Smith-Waterman Similarity Score.