title: Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences.
abstract: Rapidly growing number of sequenced genomes requires fast and accurate computational tools for analysis of different transposable elements (TEs). In this paper we focus on a rapid and reliable procedure for classification of autonomous non-LTR retrotransposons based on alignment and clustering of their reverse transcriptase (RT) domains. Typically, the RT domain protein sequences encoded by different non-LTR retrotransposons are similar to each other in terms of significant BLASTP E-values. Therefore, they can be easily detected by the routine BLASTP searches of genomic DNA sequences coding for proteins similar to the RT domains of known non-LTR retrotransposons. However, detailed classification of non-LTR retrotransposons, i.e. their assignment to specific clades, is a slow and complex procedure that is not formalized or integrated as a standard set of computational methods and data. Here we describe a tool (RTclass1) designed for the fast and accurate automated assignment of novel non-LTR retrotransposons to known or novel clades using phylogenetic analysis of the RT domain protein sequences. RTclass1 classifies a particular non-LTR retrotransposon based on its RT domain in less than 10 min on a standard desktop computer and achieves 99.5% accuracy. RT1class1 works either as a stand-alone program installed locally or as a web-server that can be accessed distantly by uploading sequence data through the internet (http://www.girinst.org/RTphylogeny/RTclass1).
authors: Genetic Information Research Institute, 1925 Landings Dr, Mountain View, CA 94041, USA. vladimir@girinst.org
authors: Vladimir V
authors: VV
authors: Kapitonov
authors: Sébastien
authors: S
authors: Tempel
authors: Jerzy
authors: J
authors: Jurka
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D002965:Classification / Q000379:methods*; D008957:Models, Genetic; D010802:Phylogeny; D017434:Protein Structure, Tertiary / Q000235:genetics; D012194:RNA-Directed DNA Polymerase / Q000737:chemistry / Q000235:genetics*; D015203:Reproducibility of Results; D018626:Retroelements / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods; D020079:Terminal Repeat Sequences / Q000235:genetics
chemical_list: D018626:Retroelements; D012194:RNA-Directed DNA Polymerase