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Fig. 1 | Mobile DNA

Fig. 1

From: Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats

Fig. 1

Overview of Look4LTRs. Our tool takes one genome or a group of related genomes as the input and outputs Long Terminal Repeat (LTR) retrotransposons. Five modules comprise Look4LTRs: (i) the scorer module, (ii) the merger module, (iii) the detector module, (iv) the matcher module, and (v) the filter module. The scorer module scores the genomes by nearby, matching k-mers. The merger module uses the scores to begin assembling potential LTRs. The detector module uses repeat content learned by Red (a tool for detecting all types of repeats uncategorized) from the genome(s) to finish assembling potential LTRs. The matcher module matches LTRs to each other to form LTR-retrotransposon candidates. The filter module removes candidates that fail to meet one of our confirmation criteria, e.g., the presence of a polypurine tract

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Mobile DNA

ISSN: 1759-8753