Homepage of the first author.

New: GWAMAR it is our new software for identifying drug resistance associated mutations. The webpage is still currently construction. GWAMAR: Genome-wide assessment of mutations associated with drug resistance in bacteria

Due to the fast progress in high-throughput sequencing technologies, the number of bacterial sequences grows rapidly (Loman et al. Nature Reviews Microbiology, 2012). This enables new interesting comparative genome analyses. On the other hand, we observe a lot of inconsistencies in genome annotations among bacterial strains. It has been shown that a wide range of comparative analyses may be complicated or biased due to the common inconsistencies in genome annotations among closely related bacterial strains (Derrick E. Wood et al. Biology Direct, 2012, John Dunbar et al. BMC Genomics, 12(1):125, 2011). It has also been shown that the use of the same tool to annotate a set of bacterial genomes increases annotation consistency ( John Dunbar et al. BMC Genomics, 12(1):125, 2011), which can be further improved by comparative annotation among multiple genomes (Poptsova et al., Microbiology, 2010). However, even though there are many annotation tools dedicated to a single genome, there are relatively few tools supporting comparative annotation and analysis of multiple bacterial genomes

We have developed eCAMBer, a tool efficiently supporting comparative analysis of multiple bacterial strains within the same species (BMC Bioinformatics 2014). In this work we achieve three major goals. First, eCAMBer is a highly optimized revision of our earlier tool, CAMBer (Wozniak et al. BMC Genomics 2011, 12(Suppl 2):S6), scaling it up for significantly larger datasets comprising hundreds of bacterial strains. Second, eCAMBer is capable of identifying and resolving annotation inconsistencies. Finally, eCAMBer improves the overall quality of annotations.

eCAMBer works in two phases. First, it unifies annotations of closely related species by homology transfer in the closure procedure. Second, eCAMBer identifies and tries to resolve annotation inconsistencies in the three procedures: (i) the refinement procedure for splitting homologous gene families into orthologous gene clusters; (ii) the TIS voting procedure for selecting the most reliable TIS; (iii) the clean up procedure for removal of gene clusters that are likely to be annotation errors propagated during the closure procedure.

This current work is also related to our another tool, called CAMBerVis (Bioinformatics 2011). In that work we developed a tool for simultaneous visualization of multiple bacterial strains, with a special focus on visualization of annotation inconsistencies. The tool developed in this work, eCAMBer, supports compatibility with CAMBerVis by producing appropriate input.

Details of the methodology are described in the eCAMBer paper.

Here is available the webpage of the old version of eCAMBer, called CAMBer.