Detection of transposable elements by their compositional bias

BMC Bioinformatics
Olivier AndrieuHadi Quesneville

Abstract

Transposable elements (TE) are mobile genetic entities present in nearly all genomes. Previous work has shown that TEs tend to have a different nucleotide composition than the host genes, either considering codon usage bias or dinucleotide frequencies. We show here how these compositional differences can be used as a tool for detection and analysis of TE sequences. We compared the composition of TE sequences and host gene sequences using probabilistic models of nucleotide sequences. We used hidden Markov models (HMM), which take into account the base composition of the sequences (occurrences of words n nucleotides long, with n ranging here from 1 to 4) and the heterogeneity between coding and non-coding parts of sequences. We analyzed three sets of sequences containing class I TEs, class II TEs and genes respectively in three species: Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana. Each of these sets had a distinct, homogeneous composition, enabling us to distinguish between the two classes of TE and the genes. However the particular base composition of the TEs differed in the three species studied. This approach can be used to detect and annotate TEs in genomic sequences and complements the current ho...Continue Reading

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Citations

Apr 8, 2009·Bioinformatics·György AbrusánWojciech Makalowski
May 4, 2011·BMC Bioinformatics·Ryan C KennedyGregory R Madey
May 25, 2011·BMC Genomics·Rita D Fernández-MedinaJosé M C Ribeiro
Aug 22, 2006·BMC Genomics·Hadi QuesnevilleDominique Anxolabéhère
Dec 20, 2008·BMC Genomics·Vini Pereira
Aug 20, 2005·PLoS Computational Biology·Hadi QuesnevilleDominique Anxolabehere
Jul 20, 2007·Chemical Reviews·Haixu Tang
Feb 23, 2010·Genomics, Proteomics & Bioinformatics·Jia Jia, Qingzhong Xue

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Software Mentioned

Objective Caml
REPBASE UPDATE
BLASTER
BDGP
BLAST
BLASTN

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