Abstract
BackgroundInconsistencies are often observed in the genome annotations of bacterial strains. Moreover, these inconsistencies are often not reflected by sequence discrepancies, but are caused by wrongly annotated gene starts as well as mis-identified gene presence. Thus, tools are needed for improving annotation consistency and accuracy among sets of bacterial strain genomes.ResultsWe have developed eCAMBer, a tool for efficiently supporting comparative analysis of multiple bacterial strains within the same species. eCAMBer is a highly optimized revision of our earlier tool, CAMBer, scaling it up for significantly larger datasets comprising hundreds of bacterial strains. eCAMBer works in two phases. First, it transfers gene annotations among all considered bacterial strains. In this phase, it also identifies homologous gene families and annotation inconsistencies. Second, eCAMBer, tries to improve the quality of annotations by resolving the gene start inconsistencies and filtering out gene families arising from annotation errors propagated in the previous phase.ConculsionseCAMBer efficiently identifies and resolves annotation inconsistencies among closely related bacterial genomes. It outperforms other competing tools both in terms of running time and accuracy of produced annotations. Software, user manual, and case study results are available at the project website: http://bioputer.mimuw.edu.pl/ecamber.
Highlights
Inconsistencies are often observed in the genome annotations of bacterial strains
Results and discussion we present the results of our experiments, which demonstrate that: (i) eCAMBer is much more efficient than CAMBer, Mugsy-Annotator and the GMV pipeline; (ii) it scales well to large datasets; (iii) it improves annotation consistency; (iv) it improves annotation accuracy; and (v) eCAMBer outperforms Mugsy-Annotator and the GMV pipeline in terms of accuracy
Large case studies We examine the scalability of eCAMBer to large datasets by running it on 10 datasets for the 10 species with the highest number of sequenced strains in the PATRIC database [2], in the 16 March 2013 release
Summary
Inconsistencies are often observed in the genome annotations of bacterial strains. These inconsistencies are often not reflected by sequence discrepancies, but are caused by wrongly annotated gene starts as well as mis-identified gene presence. Tools are needed for improving annotation consistency and accuracy among sets of bacterial strain genomes. It has been argued that most of these inconsistencies are not reflected by sequence discrepancies, but arise as a result of different annotation methodologies applied by different laboratories [10,14]. As we will observe later in section “Annotation consistency”, these annotation inconsistencies among closely related genomes can even arise from annotations produced by the same annotation tool or made by the same laboratory
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