MGERT: a pipeline to retrieve coding sequences of mobile genetic elements from genome assemblies.

ABSTRACT:

Background

Genomes of eukaryotes are inhabited by myriads of mobile genetic elements (MGEs) - transposons and retrotransposons - which play a great role in genome plasticity and evolution. A lot of computational tools were developed to annotate them either in genomic assemblies or raw reads using de novo or homology-based approaches. But there has been no pipeline enabling users to get coding and flanking sequences of MGEs suitable for a downstream analysis from genome assemblies.

Results

We developed a new pipeline, MGERT (Mobile Genetic Elements Retrieving Tool), that automates all the steps necessary to obtain protein-coding sequences of mobile genetic elements from genomic assemblies even if no previous knowledge on MGE content of a particular genome is available.

Con

SUBMITTER: Guliaev AS 

PROVIDER: S-EPMC6515669 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature