CAMBer: an approach to support comparative analysis of multiple bacterial strains

Woźniak, Michał; Wong, Limsoon; Tiuryn, Jerzy

doi:10.1186/1471-2164-12-s2-s6

Cited by 25 publications

(16 citation statements)

References 23 publications

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“…First, we compare the efficiency of eCAMBer and CAMBer by running the closure procedure for both tools on four datasets from our previous work on CAMBer [11]. All computations in this experiment were performed on the same desktop machine with 4 processor cores being used.…”

Section: Resultsmentioning

confidence: 99%

“…•The percentage of identity of the hit (calculated as the number of identities divided by the query sequence length, times 100) is above a length-dependent threshold given by the adaptation of the HSSP curve introduced in our previous work [11], defined by the parameter n t (in the default setting n t =60.5).…”

Section: Methodsmentioning

confidence: 99%

“…Here, we also recall the notion of a multigene , introduced in our previous work [11], to account for the situation when multiple ORFs share the same stop codon in the annotations produced during the closure procedure . These ORFs are called multigene elements and represent putative gene translation units.…”

Section: Methodsmentioning

confidence: 99%

“…Second, we recall the definition of the multigene consolidation graph , introduced in our previous work [11]. In this graph G M =( V M , E M ) each node m ∈ V M represents a multigene in

M_{s}^{c}

, for some s ∈ S .…”

Section: Methodsmentioning

confidence: 99%

“…In our previous work, we developed CAMBer [11], a tool conceptually similar to Mugsy-Annotator and the GMV pipeline. It supports comparative analysis of multiple bacterial strains.…”

Section: Introductionmentioning

confidence: 99%

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eCAMBer: efficient support for large-scale comparative analysis of multiple bacterial strains

2014

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…Second, we recall the definition of the multigene consolidation graph , introduced in our previous work [11]. In this graph G M =( V M , E M ) each node m ∈ V M represents a multigene in

M_{s}^{c}

, for some s ∈ S .…”

Section: Methodsmentioning

confidence: 99%

“…In our previous work, we developed CAMBer [11], a tool conceptually similar to Mugsy-Annotator and the GMV pipeline. It supports comparative analysis of multiple bacterial strains.…”

Section: Introductionmentioning

confidence: 99%

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