Inferring transposons activity chronology by TRANScendence - TEs database and de-novo mining tool

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. Therefore the software for genome-wide detection and anal...

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Bibliographic Details
Published in:BMC bioinformatics 2017-10, Vol.18 (Suppl 12), p.422-422, Article 422
Main Authors: Startek, Michał Piotr, Nogły, Jakub, Gromadka, Agnieszka, Grzebelus, Dariusz, Gambin, Anna
Format: Article
Language:English
Subjects:
Alfalfa
Algorithms
Annotations
Chronology
Classification
Computer applications
Evolution
Evolutionary genetics
Evolutionary history
Genetics
Genomes
Hill-climbing algorithm
Insects
Nesting
Software
Transcendence
Transposable elements
Transposons
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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. Therefore the software for genome-wide detection and analysis of TEs is of great interest. Here 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. TRANScendence 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.
ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-017-1824-4