Efficient algorithms and software for detection of full-length LTR retrotransposons

Abstract

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 compared to existing software. Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05) 0-7695-2344-7/05 $20.00 © 2005 IEEE Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05) 0-7695-2344-7/05 $20.00

LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons

“…These results have made ab initio computer discovery of LTR elements possible. However, tools for ab initio detection of LTR retrotransposons are still very limited: to the best of our knowledge, only two programs, LTR_STRUC (17) and LTR_par (18), have been reported, none of them being a web server.…”

De novo identification of LTR retrotransposons in eukaryotic genomes

“…The sequence-based LTR finding method, as described previously [24] or used in step 1 in our program, may miss some old retroelements, i.e. those elements containing pairs of LTRs with lower identities.…”

“…Our approach to finding these young intact LTR retroelements is equivalent to finding pairs of highly similar short subsequences (LTRs, between 100 and 1000 bps long) located within a range of distance (between 1000 to 20000) from the given genome sequence. We adopted a fast approximate string matching algorithm similar to that previously reported [24]. The entire procedure consists of three heuristic steps (Figure 8).…”

“…C. elegans [14], D. melanogaster [15,16], mouse [17] and rice [18]. Software tools, such as LTR_STRUC [19], and a newly developed one [20] were developed to speed up the screening process. However, they were based on sequence characteristics derived from known LTR retroelements.…”

Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes

“…According to Lerat (2009), LTRharvest and Find_LTR are very successful programs in locating known LTR retrotransposons, but each introduced a high number of false positives (Ellinghaus et al 2008;Rho et al 2007); LTR_STRUC has very high accuracy, but its sensitivity is relatively low (McCarthy and McDonald 2003). Other tools for retroelements include LTR_par, RetroTector, TSDFinder, SINEDR, RTAnalyzer, and MGEScan-non-LTR (Szak et al 2002;Rho and Tang 2009;Xu and Wang 2007;Lucier et al 2007;Kalyanaraman and Aluru 2006;Sperber et al 2007;Sperber et al 2009). MITEs have the same signature sets as those for DNA TEs; because homology-based approaches are often not feasible, MITEs are frequently identified using signature-based methods.…”