Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences

Saha, S., Bridges, S., Magbanua, Z. V., & Peterson, D. G. (2008). Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences. Tropical Plant Biology. Springer New York. 1(1), 85-96.

It has become clear that dispersed repeat sequences have played multiple roles in eukaryotic genome evolution including increasing genetic diversity through mutation, inducing changes in gene expression, and facilitating generation of novel genes. Growing recognition of the importance of dispersed repeats has fueled development of computational tools designed to expedite discovery and classification of repeats. Here we review major existing repeat exploration tools and discuss the algorithms utilized by these tools. Special attention is devoted to ab initio programs, i.e., those tools that do not rely upon previously identified repeats to find new repeat elements. We conclude by discussing the strengths and weaknesses of current tools and highlighting additional approaches that may advance repeat discovery/characterization.