An External Memory Approach to Compute the Statistics of Maximal Repeats from Whole Genome Sequences

Abstract

The objective of this paper is to develop an external memory approach to extract the maximal repeats from whole genome sequences with the statistics of these re- peats across classes, where the definition of a class is determined on what kind of statis- tics one wants to compute. We proposed a heuristic method consisted of a bucket- sort-like approach and the Chinese term ex- traction approach. The former was used to sort the suffixes of DNA sequences stored in files and the later was used to extract max- imal repeats by scanning the sorted suffixes while computing the statistics of these re- peats. The statistics of these repeats across classes might be useful for sequence classi- fication and species identification.