MITE Digger, an efficient and accurate algorithm for genome wide discovery of miniature inverted repeat transposable elements.

ABSTRACT:

Background

Miniature inverted repeat transposable elements (MITEs) are abundant non-autonomous elements, playing important roles in shaping gene and genome evolution. Their characteristic structural features are suitable for automated identification by computational approaches, however, de novo MITE discovery at genomic levels is still resource expensive. Efficient and accurate computational tools are desirable. Existing algorithms process every member of a MITE family, therefore a major portion of the computing task is redundant.

Results

In this study, redundant computing steps were analyzed and a novel algorithm emphasizing on the reduction of such redundant computing was implemented in MITE Digger. It completed processing the whole rice genome sequence database in ~15 hou

SUBMITTER: Yang G 

PROVIDER: S-EPMC3680318 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature