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Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity

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ModuleOrganizer: detecting modules in families of transposable elements.

Sebastien Tempel¹, Christine Rousseau, Fariza Tahi

¹IBISC, Tour Evry 2, 523 Place des Terrasses del'Agora, 91000 Evry, France.

BMC Bioinformatics

|September 24, 2010

Summary

We introduce transposable element modules, flexible motifs built on maximal repeats, to analyze sequence variations in eukaryotic genomes. This new method offers a sensitive approach for studying complex genomic rearrangements in transposable element families.

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Published on: December 22, 2017

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Eukaryotic genomes contain transposable elements (TEs), which can comprise a significant portion of genomic DNA.
TEs undergo various genomic events like mutations, copies, and deletions during transposition.
Characterizing complex TE rearrangements is challenging with traditional sequence alignment methods.

Purpose of the Study:

To develop a novel method for analyzing sequence variations and rearrangements in transposable element families.
To introduce the concept of transposable element modules for a more flexible analysis of TE architecture.
To provide a computational tool for identifying and characterizing TE transformations.

Main Methods:

Introduced the concept of a transposable element module, defined as a flexible motif built on a succession of maximal repeats.
Developed an assembly method using exact maximal repeats to construct these modules from sequence sets.
Generated a graphical representation of sequences segmented into modules for flexible analysis of variations.

Main Results:

Demonstrated the method's effectiveness using the Foldback transposable element family in Drosophila melanogaster.
Showed increased sensitivity compared to multiple alignment methods for highly variable sequences.
Identified novel copies of varying sizes and diverse module combinations in AtREP21 and SIDER2 families.

Conclusions:

The transposable element module approach provides a sensitive and flexible method for analyzing complex TE variations.
The developed method reveals new insights into TE evolution and genomic rearrangements.
The ModuleOrganizer tool is publicly available for researchers.