ArticleBMC bioinformatics2004
Detection of transposable elements by their compositional bias.
Article in BMC bioinformatics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 38 citations in OpenAlex.
- On the Base Composition of Transposable Elements.International journal of molecular sciences · 2022Review
- Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons.Mobile DNA · 2020Article
- A machine learning based framework to identify and classify long terminal repeat retrotransposons.PLoS computational biology · 2018Article
- Screening for clusters of charge in human virus proteomes.BMC genomics · 2016Article
- Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.BMC bioinformatics · 2015Article
- Deep investigation of Arabidopsis thaliana junk DNA reveals a continuum between repetitive elements and genomic dark matter.PloS one · 2014Article
- TE-Locate: A Tool to Locate and Group Transposable Element Occurrences Using Paired-End Next-Generation Sequencing Data.Biology · 2012Article
- Novel transposable elements from Anopheles gambiae.BMC genomics · 2011Article
- An automated homology-based approach for identifying transposable elements.BMC bioinformatics · 2011Article
- Codon usage biases of transposable elements and host nuclear genes in Arabidopsis thaliana and Oryza sativa.Genomics, proteomics & bioinformatics · 2009Article
- Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes.Genome biology and evolution · 2009Article
- Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome.BMC genomics · 2009Article
- Automated paleontology of repetitive DNA with REANNOTATE.BMC genomics · 2008Article
- RetroPred: A tool for prediction, classification and extraction of non-LTR retrotransposons (LINEs & SINEs) from the genome by integrating PALS, PILER, MEME and ANN.Bioinformation · 2008Article
- Article
- Combined evidence annotation of transposable elements in genome sequences.PLoS computational biology · 2005Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTransposable 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.
resultsWe 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.
conclusionsThis approach can be used to detect and annotate TEs in genomic sequences and complements the current homology-based TE detection methods. Furthermore, the HMM method is able to identify the parts of a sequence in which the nucleotide composition resembles that of a coding region of a TE. This is useful for the detailed annotation of TE sequences, which may contain an ancient, highly diverged coding region that is no longer fully functional.
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