A New AB Initio Repeats Finding Algorithm for Reference Genome

It has become clear that repetitive sequences have played multiple roles in eukaryotic genome evolution. However, identification of repetitive elements can be difficult in the ab initio manner from reference sequence. Currently, some classical ab initio tools of finding repeats have already presented. The completeness and accuracy of detecting repeats of them are very low and need to be improved. To this end, we proposed a complete and accurate ab initio repeat finding tool, named UnSaReper, which is based on unbiased sampling and dynamic overlapping extension strategy. The performances of UnSaReper are compared in human genome data Hg19 with RepeatScout and RepeatFinder. The results indicate the following conclusions: 1) The completeness of UnSaReper is the best one in almost all chromosomes; 2) In terms of total size, UnSaReper is also more powerful than others. Consequently, UnSaReper is a complete and accurate ab initio repeat finding tool.