Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming.
CONCLUSIONS
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 algorithm version and the gap opening/extension penalties. We hope that this software will be useful to teachers and students of bioinformatics courses, as well as researchers who implement the DP algorithm for diverse applications.


METHODS
The software is freely available at: http:/melolab.org/sat. The software is written in the Java computer language, thus it runs on all major platforms and operating systems including Windows, Mac OS X and LINUX.


BACKGROUND
All inquiries or comments about this software should be directed to Francisco Melo at fmelo@bio.puc.cl.
Ibarra
Ignacio L
IL
Laboratorio de Bioinformática Molecular, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.
Melo
Francisco
F
D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D011381:Programming Languages; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
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