Abstract
BackgroundThe constant progress in sequencing technology leads to ever increasing amounts of genomic data. In the light of current evidence transposable elements (TEs for short) are becoming useful tools for learning about the evolution of host genome. Therefore the software for genome-wide detection and analysis of TEs is of great interest.ResultsHere we describe the computational tool for mining, classifying and storing TEs from newly sequenced genomes. This is an online, web-based, user-friendly service, enabling users to upload their own genomic data, and perform de-novo searches for TEs. The detected TEs are automatically analyzed, compared to reference databases, annotated, clustered into families, and stored in TEs repository. Also, the genome-wide nesting structure of found elements are detected and analyzed by new method for inferring evolutionary history of TEs.We illustrate the functionality of our tool by performing a full-scale analyses of TE landscape in Medicago truncatula genome.ConclusionsTRANScendence is an effective tool for the de-novo annotation and classification of transposable elements in newly-acquired genomes. Its streamlined interface makes it well-suited for evolutionary studies.
Highlights
The constant progress in sequencing technology leads to ever increasing amounts of genomic data
The latter tool focuses on long terminal repeat (LTR) retrotransposons and more importantly is no longer unavailable to use at PlantGDB site
On the other hand the validation on real datasets is much more challenging, as there are very few available data concerning the evolutionary history of Transposable elements (TEs) families
Summary
The constant progress in sequencing technology leads to ever increasing amounts of genomic data. In the light of current evidence transposable elements (TEs for short) are becoming useful tools for learning about the evolution of host genome. Transposable elements (TEs) are genetic entities capable of changing their genomic localization. They constitute a significant portion of eucaryotic genomes. Class I gropus retrotransposons, i.e. elements transposing via an RNA intermediate using a ‘copy and paste’ mechanism. Class II comprises DNA transposons that are being physically excised from the donor site upon mobilization and transpose through a ‘cut and paste’ mechanism. The role of transposable elements in genome evolution was previously marginalized and underestimated. Nowadays these ubiquitous and widespread mobile genetic
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