PhRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats.

ABSTRACT:

Motivation

Transposable elements (TEs) and repetitive DNA make up a sizable fraction of Eukaryotic genomes, and their annotation is crucial to the study of the structure, organization, and evolution of any newly sequenced genome. Although RepeatMasker and nHMMER are useful for identifying these repeats, they require a pre-compiled repeat library-which is not always available. De novo identification tools such as Recon, RepeatScout or RepeatGluer serve to identify TEs purely from sequence content, but are either limited by runtimes that prohibit whole-genome use or degrade in quality in the presence of substitutions that disrupt the sequence patterns.

Results

phRAIDER is a de novo TE identification tool that address the issues of excessive runtime without sacrificing sensitiv

SUBMITTER: Schaeffer CE 

PROVIDER: S-EPMC4908342 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature