Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes.

ABSTRACT: LTR-retrotransposons are the most abundant repeat sequences in plant genomes and play an important role in evolution and biodiversity. Their characterization is of great importance to understand their dynamics. However, the identification and classification of these elements remains a challenge today. Moreover, current software can be relatively slow (from hours to days), sometimes involve a lot of manual work and do not reach satisfactory levels in terms of precision and sensitivity. Here we present Inpactor2, an accurate and fast application that creates LTR-retrotransposon reference libraries in a very short time. Inpactor2 takes an assembled genome as input and follows a hybrid approach (deep learning and structure-based) to detect elements, filter partial sequences and finally classif

SUBMITTER: Orozco-Arias S 

PROVIDER: S-EPMC9851300 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature