Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming.

ABSTRACT:

Summary

Dynamic programming (DP) is a general optimization strategy that is successfully used across various disciplines of science. In bioinformatics, it is widely applied in calculating the optimal alignment between pairs of protein or DNA sequences. These alignments form the basis of new, verifiable biological hypothesis. Despite its importance, there are no interactive tools available for training and education on understanding the DP algorithm. Here, we introduce an interactive computer application with a graphical interface, for the purpose of educating students about DP. The program displays the DP scoring matrix and the resulting optimal alignment(s), while allowing the user to modify key parameters such as the values in the similarity matrix, the sequence alignment algorit

SUBMITTER: Ibarra IL 

PROVIDER: S-EPMC2887054 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature