Exact sequence matches in genomic studies

Abstract

The purpose of this article is to review usage of exact sequence matches in different field of genomic studies. Methods. The presentation is built in the form of a brief review of clearly non-exhaustive list of works in which the authors inferred biological knowledge using statistical properties of exact matches between different genomic texts or self-matches along the same genomic sequence. Results. Often, in genomic studies, different genomic loci exhibit different statistical properties, while their boundaries are not known a priory. In such cases we conclude that studying statistical properties of exact sequence matches is a useful alternative to other methods, for instance, based on arbitrary-size (non-)sliding windowing of the genome. Conclusion. This review demonstrates that exact sequences matches are not only an important auxiliary alignment step, but also helpful in other contexts. Their statistical properties are relatively easy to calculate analytically or numerically under various assumptions and compare to empirical data, validating models and fitting the models’ parameters.

Keywords

• genomics
• exact sequence matches
• maximal exact matches
• k-mers
• genome evolution
• horizontal gene transfer