title: De novo identification of LTR retrotransposons in eukaryotic genomes.
abstract: BACKGROUND
  LTR retrotransposons are a class of mobile genetic elements containing two similar long terminal repeats (LTRs). Currently, LTR retrotransposons are annotated in eukaryotic genomes mainly through the conventional homology searching approach. Hence, it is limited to annotating known elements.
  
  
  RESULTS
  In this paper, we report a de novo computational method that can identify new LTR retrotransposons without relying on a library of known elements. Specifically, our method identifies intact LTR retrotransposons by using an approximate string matching technique and protein domain analysis. In addition, it identifies partially deleted or solo LTRs using profile Hidden Markov Models (pHMMs). As a result, this method can de novo identify all types of LTR retrotransposons. We tested this method on the two pairs of eukaryotic genomes, C. elegans vs. C. briggsae and D. melanogaster vs. D. pseudoobscura. LTR retrotransposons in C. elegans and D. melanogaster have been intensively studied using conventional annotation methods. Comparing with previous work, we identified new intact LTR retroelements and new putative families, which may imply that there may still be new retroelements that are left to be discovered even in well-studied organisms. To assess the sensitivity and accuracy of our method, we compared our results with a previously published method, LTR_STRUC, which predominantly identifies full-length LTR retrotransposons. In summary, both methods identified comparable number of intact LTR retroelements. But our method can identify nearly all known elements in C. elegans, while LTR_STRUCT missed about 1/3 of them. Our method also identified more known LTR retroelements than LTR_STRUCT in the D. melanogaster genome. We also identified some LTR retroelements in the other two genomes, C. briggsae and D. pseudoobscura, which have not been completely finished. In contrast, the conventional method failed to identify those elements. Finally, the phylogenetic and chromosomal distributions of the identified elements are discussed.
  
  
  CONCLUSIONS
  We report a novel method for de novo identification of LTR retrotransposons in eukaryotic genomes with favorable performance over the existing methods.
authors.affiliation: Department of Computer Science, Indiana University, Bloomington, IN 47405, USA. mrho@indiana.edu
authors.forename: Mina
authors.initials: M
authors.lastname: Rho
authors.forename: Jeong-Hyeon
authors.initials: JH
authors.lastname: Choi
authors.forename: Sun
authors.initials: S
authors.lastname: Kim
authors.forename: Michael
authors.initials: M
authors.lastname: Lynch
authors.forename: Haixu
authors.initials: H
authors.lastname: Tang
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D002874:Chromosome Mapping; D016000:Cluster Analysis; D004330:Drosophila / Q000235:genetics; D005057:Eukaryotic Cells; D016678:Genome; D008969:Molecular Sequence Data; D010802:Phylogeny; D018626:Retroelements / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software; D020079:Terminal Repeat Sequences / Q000235:genetics*
chemical_list: D018626:Retroelements