MGEScan

MGEScan is a suite of two software tools MGEScan-LTR and MGEScan-non-LTR.

MGEScan-LTR is a software that can identify new LTR retrotransposons without relying on a library of known elements. It uses approximate string matching technique and protein domain analysis to detect intact LTR retrotransposons. In addition, it identifies partially deleted or solo LTRs using profile Hidden Markov Models (pHMMs).

MGEScan-non-LTR is a software for the identification of non-LTR retrotransposons in genomic sequences, following a computational approach inspired by a generalized hidden Markov model (GHMM).

References:
1. M. Rho et al., "De novo identification of LTR retrotransposons in eukaryotic genomes", BMC Genomics (2007) 8:90.

2. M. Rho and H. Tang, "MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes", Nucleic Acids Research (2009) 37:21.