RTanalyzer

RTanalyzer analyzes L1-mediated retrotransposition in mammalian genomes by detecting characteristic molecular signatures and quantifying the likelihood that a genomic sequence originated from a retrotransposition event.

Key Features:

• Signature Detection: Identifies sequences indicative of L1-mediated retrotransposition by detecting Target Site Duplication (TSD), polyadenylation signal/poly(A) at the 3' end, and endonuclease cleavage sites at the 5' end.
• Retrotransposition Scoring: Calculates an overall retrotransposition score that quantifies the likelihood a sequence resulted from L1-mediated insertion based on detected signatures.
• Database Integration and Sequence Retrieval: Uses BLAST to search genomic databases and retrieves each hit together with flanking sequences for downstream signature analysis.

Scientific Applications:

• Trace Evolutionary Histories: Reconstructs the contribution of L1-mediated insertions to mammalian genome evolution by identifying and scoring retrotransposition events.
• Study Non-Autonomous Retrotransposons: Detects insertion features of non-autonomous elements that rely on autonomous L1 proteins for mobilization.
• Identify Functional Impacts: Enables investigation of how retrotransposition insertions may affect gene function or regulation by locating and characterizing insertion events.

Methodology:

Performs BLAST-based sequence searches of genomic databases, examines retrieved sequences for TSD, polyA tails, and endonuclease cleavage sites, and computes a retrotransposition score from the identified signatures.