Identification and Analysis of Transposable Elements in Genomic Sequences
Laurent Modolo and Emmanuelle Lerat
from: Genome Analysis: Current Procedures and Applications (Edited by: Maria S. Poptsova). Caister Academic Press, U.K. (2014)
Genome sequences are composed of different compartments, among which transposable elements (TEs) represent one of the most important. Not only do these elements correspond to a particularly large proportion of genomes, they are also involved in different mechanisms implicated in the evolution of genomes, such as chromosome rearrangement and gene innovation. Thus, the precise determination of TEs in genomes is of significant importance. This step is becoming more and more complex with the emergence of new types of sequence data coming from next-generation sequencing (NGS) technologies. In this chapter, we present the current status of bioinformatic developments made in the detection and analysis of TEs in genomic sequences. We first present the classic tools dedicated to the identification of TEs in classic genomic data, which originate from whole genome sequences. Because these sequences are significantly different from the new types of sequences generated by NGS and because the problem of repeats in these data is not trivial, we then present how it is possible to handle TEs in NGS data. We also provide some examples of tools designed to answer particular questions about TEs using NGS data and how these types of data are particularly valuable for deepening our knowledge of the dynamics of TEs. Although this is a still a fast-growing field for which new developments are made every day, we hope to provide a broader view of what currently exists in this field and what allows for TE analyses in genomic sequences read more ...