Document Type
Article
Original Publication Date
2015
Journal/Book/Conference Title
Bioinformation
Volume
11
Issue
6
DOI of Original Publication
10.6026/97320630011276
Date of Submission
December 2015
Abstract
The newest technologies for DNA sequencing have led to the determination of the primary structure of the genomes of organisms, mainly prokaryotes, with high efficiency and at lower costs. However, the presence of regions with repetitive sequences, in addition to the short reads produced by the Next-Generation Sequencing (NGS) platforms, created a lot of difficulty in reconstructing the original genome in silico. Thus, even today, genome assembly continues to be one of the major challenges in bioinformatics specifically when repetitive sequences are considered. In this paper, we present an approach to assemble repetitive regions in prokaryotic genomes. Our methodology enables (i) the identification of these regions through visual tools, (ii) the characterization of sequences on the extremities of gaps and (iii) the extraction of consensus sequences based on mapping of raw data to a reference genome. We also present a case study on the assembly of regions that encode ribosomal RNAs (rRNA) in the genome of Corynebacterium ulceransFRC11, in order to show the efficiency of the strategies presented here. The proposed methods and tools will help in finishing genome assemblies, besides reducing the running time and associated costs.
Availability
All scripts are available at http://github.com/dcbmariano/maprepeat
Rights
Copyright © 2015 Biomedical Informatics: This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.
Is Part Of
VCU Computer Science Publications
Comments
Originally published at http://dx.doi.org/10.6026/97320630011276