moduleorganizer

moduleorganizer organizes DNA sequences into modular representations to analyze and characterize transposable elements and their structural transformations in eukaryotic genomes.

Key Features:

• Segmentation into Domains: Segments DNA sequences into distinct domains based on their structural characteristics.
• Classification Based on Domains: Classifies sequences according to the segmented domains to enable categorization and comparison within families.
• Transposable Element Modules: Defines transposable element modules as flexible motifs present in at least two sequences from a family of transposable elements.
• Maximal Repeats Construction: Constructs modules by assembling sets of exact maximal repeats from a collection of sequences.
• Graphical Representation: Provides a graphical view that segments sequences into modules for visual analysis of transformations and rearrangements.
• Sensitivity to Variable Sequences: Shows enhanced sensitivity compared to traditional multiple alignment methods for highly variable sequences.
• Detection of Variable Copies and Combinations: Identifies new copies of varying sizes and novel combinations of modules.

Scientific Applications:

• Transposable Element Analysis: Enables detailed analysis of transposable elements that comprise substantial fractions of eukaryotic genomes.
• Evolutionary Dynamics: Supports investigation of the evolutionary dynamics and functional implications of TE families.
• Discovery of Novel Elements: Facilitates detection of previously unrecognized TE copies and novel module combinations.
• Non-autonomous Transposon Analysis: Accommodates analysis of complex rearrangements in transposons that have lost protein-coding capacity.
• Case Studies: Has been applied to families such as the Foldback family in Drosophila melanogaster, AtREP21, and SIDER2.

Methodology:

Assembles sets of exact maximal repeats from collections of sequences to create transposable element modules; defines modules as repeats present in at least two family members; segments sequences into domains based on structural characteristics and classifies sequences according to those domains.