Detection of transposable elements by their compositional bias

Background: 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. Results: 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, C

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Olivier Andrieu, Anna-Sophie Fiston, Dominique Anxolabéhère, Hadi Quesneville
• Keywords: BMCBI 2004, Mobile Genetic Entities, Sequences, TE Sequences