[52] Computer analysis of nucleic acid sequences

Abstract

Publisher Summary This chapter focuses on some methods of computer analysis of sequence data. The intent is to describe the analyses and to give emphasis to the possible utility of the analysis, not to present detailed mathematics or computer science of the techniques. Computer analysis of sequences has some distinct advantages over analysis by “eye.” The computer analysis must be well defined, explicitly, so that the same search can be duplicated elsewhere. Many more cases can be examined by computer, and the calculations are done correctly. Inherent in these advantages are some important disadvantages. The computer will only do exactly what it is programmed to do. If the task is the “wrong” one, massive and correct calculations do not help. In addition, a machine will not notice a pattern it has not been programmed to notice, something at which humans excel. The sequence analyst should be aware of what the computer is doing and what is not. Computation might be useful but it should not stand alone. The computer analysis of nucleic acid sequences has produced some interesting mathematics, and some algorithms and programs useful for sequence analysis. As biology continues to gather sequence data at increasing rates and to find new fundamental questions of interest, the mathematics and computer science to solve related questions will also progress.