MGEScan-LTR / MGEScan-non-LTR v2
MGEScan-LTR is a de novo computational method identifies new LTR (long terminal repeat) retrotransposons without relying on a library of known elements. Specifically, the method identifies intact LTR retrotransposons by using an approximate string matching technique and protein domain analysis.
MGEScan-non-LTR is an computational approach to the identification of non-LTR retrotransposons in genomic sequences, based on a generalized hidden Markov model (GHMM), in which the hidden states represent the protein domains and linker regions encoded in the non-LTR retrotransposons, and their emission probabilities are modeled by profile hidden Markov models (for protein domains) and Gaussian Bayes classifiers (for linker regions), respectively.
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Nucleic Acids Res. 2009 Nov;37(21):e143.
MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes.
Rho M, Tang H.