RepeatRunner – Repeat Identification and Masking in Dipterans



RepeatRunner is a CGL-based program that integrates RepeatMasker with BLASTX to provide a comprehensive means of identifying repetitive elements. Because RepeatMasker identifies repeats by means of similarity to a nucleotide library of known repeats, it often fails to identify highly divergent repeats and divergent portions of repeats, especially near repeat edges. To remedy this problem, RepeatRunner uses BLASTX to search a database of repeat encoded proteins (reverse transcriptases, gag, env, etc…). Because protein homologies can be detected across larger phylogenetic distances than nucleotide similarities, this BLASTX search allows RepeatRunner to identify divergent protein coding portions of retro-elements and retro-viruses not detected by RepeatMasker. RepeatRunner merges its BLASTX and RepeatMasker results to produce a single, comprehensive XML-based output. It also masks the input sequence appropriately. In practice RepeatRunner has been shown to greatly improve the efficacy of repeat identifcation. RepeatRunner can also be used in conjunction with PILER-DF – a program designed to identify novel repeats – and RepeatMasker to produce a comprehensive system for repeat identification, characterization, and masking in the newly sequenced genomes.



Yandell Lab








Gene. 2007 Mar 1;389(1):1-9. Epub 2006 Oct 12.
Improved repeat identification and masking in Dipterans.
Smith CD, Edgar RC, Yandell MD, Smith DR, Celniker SE, Myers EW, Karpen GH.

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