MiteFinder: A fast approach to identify miniature inverted-repeat transposable elements on a genome-wide scale

Miniature inverted-repeat transposable element (MITE) is a type of class II non-autonomous transposable element playing a crucial role in the process of evolution in biology. Development of bioinformatics tools that are capable of effectively identifying MITEs can enable genome-wide studies of MITE patterns in eukaryotes. Here, we present a fast, accurate and memory-efficient tool, MiteFinder, for the identification of MITEs from genomics sequences. MiteFinder distinguishes itself from other existing methods by building k-mer indexes for large genomes, which can effectively identify all possible inverted repeats. To calculate the likelihood of how much a given sequence is a MITE, we introduce a log-ratio scoring model that uses the distribution of sequence pattern in two models, mite model (M) and null model (N). The results suggest that MiteFinder outperforms existing tools in both precision and recall. Besides, it is much faster and more memory-efficient than other tools in the detection. The source code is freely accessible at the website: https://github.com/screamer/miteFinder.