Tracks sequences of retrotransposed origin by scoring the signature results from an L1-mediated insertion within a genome.
Highlights:
A sequence of interest is searched for in genomic databases using BLAST.
Each hit, along with additional 5' and 3' sequences of pre-defined lengths, is saved.
RTAnalyzer searches for specific L1 retrotransposition signatures (i.e. target site duplication, endonuclease cleavage site and poly(A)), and then calculates an overall retrotransposition score.
This score represents the likelihood of a given sequence originating from a retrotransposition event involving the L1 machinery.
