Search our Database of Scientific Publications and Authors

I’m looking for a

    Details and Download Full Text PDF:
    Analysis of transposable element sequences using CENSOR and RepeatMasker.

    Methods Mol Biol 2009 ;537:323-36
    School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.
    Eukaryotic genomes are full of repetitive DNA, transposable elements (TEs) in particular, and accordingly there are a number of computational methods that can be used to identify TEs from genomic sequences. We present here a survey of two of the most readily available and widely used bioinformatics applications for the detection, characterization, and analysis of TE sequences in eukaryotic genomes: CENSOR and RepeatMasker. For each program, information on availability, input, output, and the algorithmic methods used is provided. Specific examples of the use of CENSOR and RepeatMasker are also described. CENSOR and RepeatMasker both rely on homology-based methods for the detection of TE sequences. There are several other classes of methods available for the analysis of repetitive DNA sequences including de novo methods that compare genomic sequences against themselves, class-specific methods that use structural characteristics of specific classes of elements to aid in their identification, and pipeline methods that combine aspects of some or all of the aforementioned methods. We briefly consider the strengths and weaknesses of these different classes of methods with an emphasis on their complementary utility for the analysis of repetitive DNA in eukaryotes.

    Similar Publications

    Transposable element annotation of the rice genome.
    Bioinformatics 2004 Jan;20(2):155-60
    Department of Biology, McGill University, Montreal, Quebec, H3A 1B1 Canada.
    Motivation: The high content of repetitive sequences in the genomes of many higher eukaryotes renders the task of annotating them computationally intensive. Presently, the only widely accepted method of searching and annotating transposable elements (TEs) in large genomic sequences is the use of the RepeatMasker program, which identifies new copies of TEs by pairwise sequence comparisons with a library of known TEs. Profile hidden Markov models (HMMs) have been used successfully in discovering distant homologs of known proteins in large protein databases, but this approach has only rarely been applied to known model TE families in genomic DNA. Read More
    Computational analysis of transposable element sequences.
    Methods Mol Biol 2004 ;260:59-71
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
    This chapter provides a simple guide for the computational analysis of transposable element (TE) sequences. Web links are provided for a number of sequence analysis applications, and their potential use in the analysis of TE sequences is briefly described. The level of detail provided is intended to be sufficient for a naive user to begin to analyze TE sequences in silico. Read More
    Discovering and detecting transposable elements in genome sequences.
    Brief Bioinform 2007 Nov 10;8(6):382-92. Epub 2007 Oct 10.
    Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
    The contribution of transposable elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Here we review the diversity of innovative approaches to identify and annotate TEs in the post-genomic era, covering both the discovery of new TE families and the detection of individual TE copies in genome sequences. These approaches span a broad spectrum in computational biology including de novo, homology-based, structure-based and comparative genomic methods. Read More
    Identification of transcription factor binding sites derived from transposable element sequences using ChIP-seq.
    Methods Mol Biol 2010 ;674:225-40
    School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.
    Transposable elements (TEs) form a substantial fraction of the non-coding DNA of many eukaryotic genomes. There are numerous examples of TEs being exapted for regulatory function by the host, many of which were identified through their high conservation. However, given that TEs are often the youngest part of a genome and typically exhibit a high turnover, conservation-based methods will fail to identify lineage- or species-specific exaptations. Read More