Asee peer logo

Genomic Grammars: Teaching Bioinformatics Using Language Theory

Download Paper |


2005 Annual Conference


Portland, Oregon

Publication Date

June 12, 2005

Start Date

June 12, 2005

End Date

June 15, 2005



Conference Session

Bringing Biology into Engineering

Page Count


Page Numbers

10.662.1 - 10.662.10



Permanent URL

Download Count


Request a correction

Paper Authors

author page

John Kaplan

author page

Kathleen Kaplan

Download Paper |

NOTE: The first page of text has been automatically extracted and included below in lieu of an abstract

Genomic Grammars: Teaching Bioinformatics Using Language Theory

Kathleen M. Kaplan, D.Sc., Lt Col John J. Kaplan (Ph.D., J.D.) USAF

Howard University/USAF


Language theory is an important part of engineering. It is usually taught in compiler theory, operating systems, and other courses. Therefore, the use of language theory, which is familiar to most engineering students, is a good tool to use to introduce bioinformatics.

There are three elements to a language: alphabet, grammar, and semantics. The alphabet comprises the words, the grammar defines the rules, and the semantics give the meaning of the language. With respect to genomics, the genomic alphabet has been known for a long time: in DNA it’s the set {A, C, T, G} and in RNA the set {A, C, U, G}. The words in genomics are the genes, of which many have been identified. The semantics, or meaning, of the genes may not be known though. With the rush to patent genes during the near-past, shot-gun methods and others were used. Thus, genes were identified, without understanding the genes’ specific functions. This is akin in language theory as identifying the words (genes) of the language but not their meaning (specific functions).

This paper describes grammars, not the semantics, of language theory. It also discusses the representation of genes using grammars. Furthermore, it gives examples of project assignments for engineering students.

By teaching bioinformatics using familiar tools, such as language theory, the engineering student gains knowledge of biology, bioinformatics and the relationship of engineering principles to other disciplines.

“Proceedings of the 2005 American Society for Engineering Education Annual Conference & Exposition Copyright  2005, American Society for Engineering Education”

Kaplan, J., & Kaplan, K. (2005, June), Genomic Grammars: Teaching Bioinformatics Using Language Theory Paper presented at 2005 Annual Conference, Portland, Oregon. 10.18260/1-2--14992

ASEE holds the copyright on this document. It may be read by the public free of charge. Authors may archive their work on personal websites or in institutional repositories with the following citation: © 2005 American Society for Engineering Education. Other scholars may excerpt or quote from these materials with the same citation. When excerpting or quoting from Conference Proceedings, authors should, in addition to noting the ASEE copyright, list all the original authors and their institutions and name the host city of the conference. - Last updated April 1, 2015