Lawrence D'Antonio
Abstract
In this paper we examine ways in which ideas from the exciting new field of bioinformatics can be used in an algorithms course intended for computer science majors. Bioinformatics studies biological sequences such as DNA or protein that are the building blocks of life. Algorithms that involve searching, matching, or combining such sequences are primary tools in bioinformatics. These algorithms use many key ideas that are important to the computer science major, such as dynamic programming. In addition, bioinformatics makes for an interesting and timely application that can enliven the algorithms course.
- Clote, P. and Backofen, R. Computational Molecular Biology: an Introduction. John Wiley, West Sussex, England, 2000.Google Scholar
- Cooper, N. The Human Genome Project. Univ. Science Books, Mill Valley CA, 1994.Google Scholar
- Dayhoff, M. O., Schwartz, R. M., and Orcutt, B. C. A model of evolutionary change in proteins. In Dayhoff, M. O. (ed) Atlas of Protein Sequence and Structure, vol. 5, supplement 3, National Biomedical Research Foundation, Washington, D.C., 1978.Google Scholar
- Gusfield, D. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, Cambridge, England, 1997. Google ScholarDigital Library
- Mount, D. Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2001.Google Scholar
- Needleman, S. B. and Wunsch, C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins, Journal of Molecular Biology, 48 (1970), 443--453.Google ScholarCross Ref
- Setubal J. and Meidanis, J. Introduction to Computational Molecular Biology. PWS Publishing Company. Pacific Grove, CA, 1997.Google Scholar
- Smith, T. F. and Waterman M. Identification of common molecular subsequences. Journal of Molecular Biology, 284 (1981), 195--197.Google ScholarCross Ref
- Wang, L. and Jiang T. On the complexity of multiple sequence alignment. Journal of Computational Biology 1(1994), 337--348.Google ScholarCross Ref
- Waterman, M. Introduction to Computational Biology. Chapman & Hall/CRC Press, Boca Raton, FL, 1995.Google ScholarCross Ref
- Whitehead Institute Human Genome Web Site, http://www-genome.wi.mit.edu/Google Scholar
Index Terms
- Incorporating bioinformatics in an algorithms course
Recommendations
Incorporating bioinformatics in an algorithms course
ITiCSE '03: Proceedings of the 8th annual conference on Innovation and technology in computer science educationIn this paper we examine ways in which ideas from the exciting new field of bioinformatics can be used in an algorithms course intended for computer science majors. Bioinformatics studies biological sequences such as DNA or protein that are the building ...
SnS-Align: a graphic tool for alignment of distantly related proteins
Genomic sequences for many animal species are now available in the public domain. Protein similarity search in evolutionarily distant organisms by sequence comparison often turns out to be difficult. Here, we present the Structure and Sequence Alignment ...
Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome
XSEDE '15: Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced CyberinfrastructureToday's genomics technologies generate more sequence data than ever before possible, and at substantially lower costs, serving researchers across biological disciplines in transformative ways. Building transcriptome assemblies from RNA sequencing reads ...
Comments