BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data

Abstract

BG7 is a new system for de novo bacterial, archaeal and viral genome annotation based on a new approach specifically designed for annotating genomes sequenced with next generation sequencing technologies. The system is versatile and able to annotate genes even in the step of preliminary assembly of the genome. It is especially efficient detecting unexpected genes horizontally acquired from bacterial or archaeal distant genomes, phages, plasmids, and mobile elements. From the initial phases of the gene annotation process, BG7 exploits the massive availability of annotated protein sequences in databases. BG7 predicts ORFs and infers their function based on protein similarity with a wide set of reference proteins, integrating ORF prediction and functional annotation phases in just one step. BG7 is especially tolerant to sequencing errors in start and stop codons, to frameshifts, and to assembly or scaffolding errors. The system is also tolerant to the high level of gene fragmentation which is frequently found in not fully assembled genomes. BG7 current version – which is developed in Java, takes advantage of Amazon Web Services (AWS) cloud computing features, but it can also be run locally in any operating system. BG7 is a fast, automated and scalable system that can cope with the challenge of analyzing the huge amount of genomes that are being sequenced with NGS technologies. Its capabilities and efficiency were demonstrated in the 2011 EHEC Germany outbreak in which BG7 was used to get the first annotations right the next day after the first entero-hemorrhagic E. coli genome sequences were made publicly available. The suitability of BG7 for genome annotation has been proved for Illumina, 454, Ion Torrent, and PacBio sequencing technologies. Besides, thanks to its plasticity, our system could be very easily adapted to work with new technologies in the future.

Next-Generation Annotation of Prokaryotic Genomes with EuGene-P: Application to Sinorhizobium meliloti 2011

“…In the area of prokaryotic genome annotation, existing NGS-related studies 11 have focussed on the possibly increased level of sequencing errors associated with such technologies. Here, we showed that the quality of the Sm2011 genomic sequence obtained by NGS is comparable with, if not better than, the Sm1021 genomic sequence previously generated by Sanger sequencing.…”

“…In the recent sequencing of bacterial and archeal genomes, the annotation has still been done manually owing to the lack of appropriate tools to integrate RNA-Seq data. 5 Indeed, most existing prokaryotic gene finders 6–9 or high-level bacterial annotation systems 10,11 are based on genomic sequence analysis and cannot take into account available expression data in the structural prediction. Expert annotation using RNA-Seq data has been recently facilitated by the use of integrated tools, such as VESPA 12 or MicroScope, 13 which allow to simultaneously visualize genomic, transcriptomic, proteomic or syntenic data, but the ultimate curation process still remains laborious.…”

Normal Mutation Rate Variants Arise in a Mutator (Mut S) Escherichia coli Population

“…The assemblies were done using high values for k parameter to reduce the possibility of misassembles. The prediction of genes and the functional annotation was carried out using BG7 [29]. A de novo assembly was carried out using Velvet [28].…”

Experiences in integrated data and research object publishing using GigaDB

“…The microbial genomics community around the world immediately took up the challenge to study the organism collaboratively (a process that was dubbed by some bloggers as the first "Tweenome"). Using these data, within the first 24 h of release, researchers from Birmingham University had released their own genome assembly in the same manner, and a group in Spain released analyses from a new annotation platform and set up a collaborative GitHub repository to provide a home to these analyses and data [58]. Within days of the initial release, a potential ancestral strain had been identified by a blogger in the US [51], helping clear Spanish farmers of the blame.…”