Efficient Algorithms and Software for Detection of Full-length Ltr Retrotransposons

LTR retrotransposons constitute one of the most abundant classes of repetitive elements in eukaryotic genomes. In this paper, we present a new algorithm for detection of full-length LTR retrotransposons in genomic sequences. The algorithm identifies regions in a genomic sequence that show structural characteristics of LTR retrotransposons. Three key components distinguish our algorithm from that of current software -- (i) a novel method that preprocesses the entire genomic sequence in linear time and produces high quality pairs of LTR candidates in running time that is constant per pair, (ii) a thorough alignment-based evaluation of candidate pairs to ensure high quality prediction, and (iii) a robust parameter set encompassing both structural constraints and quality controls providing users with a high degree of flexibility. Validation of both our serial and parallel implementations of the algorithm against the yeast genome indicates both superior quality and performance results when...

• Type: Journal
• Year: 2006
• Where: JBCB
• Authors: Anantharaman Kalyanaraman, Srinivas Aluru
• Keywords: Algorithm, Genomic Sequence, JBCB 2006, LTR Retrotransposons