TEENA

TEENA streamlines transposable element enrichment analysis across various model and non-model organisms by implementing an optimized pipeline that hosts genome, gene, and TE annotations for nearly one hundred species.

Key Features:

• Automated annotation retrieval: TEENA automatically retrieves corresponding genome, gene, and TE annotations when provided with genomic interval data as the only user-supplied file.
• Multi-species annotation hosting: TEENA hosts annotations for almost one hundred species, encompassing both model and non-model organisms.
• Flexible parameter configuration: TEENA provides multiple parameters to enable flexibility in analysis configuration.
• Streamlined analysis pipeline: TEENA implements an optimized pipeline that completes routine analyses in a couple of minutes.

Scientific Applications:

• TE-derived cis-element identification: TEENA identifies enriched transposable elements in distinct genomic intervals such as enhancers or transcription factor binding sites as candidates for studying TE regulatory functions.
• Transcription factor binding site analysis: TEENA enables analysis of transposable element enrichment at genomic intervals bound by distinct transcription factors.
• Enhancer analysis: TEENA supports identification of enriched transposable elements within sets of enhancers to investigate their cis-regulatory potential.

Methodology:

TEENA takes genomic interval data as input and automatically retrieves corresponding annotations to perform enrichment analysis; specific computational algorithms are not explicitly detailed in the sources.