Improving prokaryotic transposable elements identification using a combination of de novo and profile HMM methods.

ABSTRACT:

Background

Insertion Sequences (ISs) and their non-autonomous derivatives (MITEs) are important components of prokaryotic genomes inducing duplication, deletion, rearrangement or lateral gene transfers. Although ISs and MITEs are relatively simple and basic genetic elements, their detection remains a difficult task due to their remarkable sequence diversity. With the advent of high-throughput genome and metagenome sequencing technologies, the development of fast, reliable and sensitive methods of ISs and MITEs detection become an important challenge. So far, almost all studies dealing with prokaryotic transposons have used classical BLAST-based detection methods against reference libraries. Here we introduce alternative methods of detection either taking advantages of the structura

SUBMITTER: Kamoun C 

PROVIDER: S-EPMC3852290 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature