ExplorATE

ExplorATE quantifies active transposable elements in RNA-seq data by generating TE-specific indexes and applying Selective Alignment and Wicker-like criteria to distinguish actively transcribed TEs from co-transcribed elements.

Key Features:

• TE-Specific Index Creation: Generates TE-specific sequence indexes to facilitate precise quantification of transposable elements in both model and non-model organisms.
• Selective Alignment Strategy: Implements a Selective Alignment (SA) approach that uses alignment scores to distinguish co-transcribed transposons within genes from independently active TEs.
• Wicker-like Criteria Integration: Incorporates Wicker-like criteria to refine target TE sets and minimize spurious mappings.
• Efficiency and Speed: Shows high congruence with alignment-based tools while requiring less execution time in comparative analyses using simulated and real data.
• Comprehensive Analysis Capabilities: Accounts for co-transcription and multi-mapping effects during TE quantification and provides outputs for integration with downstream analytical tools in the R environment.

Scientific Applications:

• Functional analysis of transposable elements: Accurate identification and quantification of active TEs from RNA-seq to study their impact on host genomes across model and non-model organisms.
• Co-transcription and multi-mapping assessment: Disentangling co-transcribed elements from independently active TEs and accounting for multi-mapping in expression estimates.
• Method benchmarking: Comparative evaluation of TE quantification approaches using simulated and real RNA-seq data to assess congruence and execution time relative to alignment- and mapping-based tools.

Methodology:

Creates TE-specific indexes, performs Selective Alignment (SA) using alignment scores to filter co-transcribed transposons, applies Wicker-like criteria to refine target TE sets, and is implemented using R and bash scripts.