BMX: a tool for computing bacterial phyletic composition from orthologous maps

BMC Research Notes

Benard W Kulohoma¹ 

[1] Institute of Infection and Global Health, Liverpool, University of Liverpool, Liverpool, 8 West Derby Street, Liverpool L69 7BE, UK

关键词: Prokaryotes;    Core genome;    Orthologous maps;   

Others  :  1131352
DOI  :  10.1186/s13104-015-1017-z

 received in 2014-08-29, accepted in 2015-02-13,  发布年份 2015

【 摘 要 】

Background

New sequencing technologies have made it possible to explore genetic diversity at higher resolution in microbial populations. However, our understanding evolutionary relationships, and comparison of closely and distantly related bacterial genomes from these massive datasets remains a formidable challenge. Numerous clustering algorithms that group genomic data based on homology have been developed, but new tools are still required to analyse the resultant orthologous maps to understand functional genetic similarities and their phyletic patterns (patterns of presence of absence of genes).

Findings

Bacterial Makeup eXplorer (BMX) implements an algorithm that swiftly and efficiently facilitates the determination of the number of orthologs in prokaryotic genomes employing a reference free approach, which may be further exploited to transfer of gene annotations. BMX is able to integrate orthologous maps of highly diverse prokaryotic genomes therefore making it possible to perform robust and scalable, multi-platform, high quality annotation transfer and gene-by-gene composition assessment method. In addition results are presented in the form of publication quality figures.

Conclusions

BMX allows extensive data analysis of orthologous map databases to understand underlying biological relationships. Furthermore, BMX is portable across different platforms and can be installed easily. In summary, BMX allows higher resolution analysis of genomes from diverse bacterial populations

【 授权许可】

   
2015 Kulohoma; licensee BioMed Central.

【 图 表 】

Figure 1.

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