This will inevitably enhance our understanding on the virulence mechanisms, genome structure, and molecular evolution of mycobacteria. Construction and content

AG-014699 ic50 Data sources and curation MyBASE contains data from both our own experiments and public resources. There are four main types of data: 1) genome sequences with curated annotations, 2) genome polymorphism data, particularly LSPs identified among different mycobacterial genomes, 3) functional gene annotations with a specific focus on virulence genes and essential genes, and 4) predicted operons. All complete genome sequences and original annotation files were downloaded from NCBI ftp://​ftp.​ncbi.​nih.​gov/​genomes/​Bacteria. Curations were made to clarify inconsistencies resulting from different annotations provided by the original sequence providers. For Clusters of Orthologous Groups (COGs) that were inconsistently designated [24], we refined the COGs using the algorithm previously described [25]. We have recently used the NimbleGen tiling microarray method for whole-genome comparison of 13 BCG strains with subsequent confirmation by DNA re-sequencing [26]. A total of 42 deletions were identified, four of which are novel [26]. These novel deletions are believed to have an impact on virulence or immunogenicity of the corresponding BCG strains [26]. All data

and analytical results were incorporated into MyBASE. In addition to our self-generated data, other polymorphism datasets, particularly

LSPs/RDs that were included 17-DMAG (Alvespimycin) HCl in MyBASE were extracted from public literatures. After the first usage of Rapamycin microarray to study genome polymorphism in 1999 [3], a growing trend emerged to generate systematic genome polymorphism data [27–29]. We performed an extensive literature review to extract information about each LSP/RD from original experiments. We found inconsistencies between the nomenclature of LSPs (RDs) used by different groups and so to avoid further confusion, we have kept the original nomenclature from each group. However, we have provided the reference information and a hyperlink to the PubMed entry for each LSP/RD dataset. Virulence, essentiality and other functional annotations of mycobacterial genes were extracted and corrected through data mining of public resources [10–14, 30]. Virulence of mycobacterial genes was evaluated by phenotypic outcomes observed from animal and cellular models of M. tb infections (e.g., mouse, guinea pig, macrophages, etc.) for the corresponding mutants [14]. Recently, with the success of genetic manipulation of mycobacterial genes, a number of new virulence factors have been uncovered [31–35]. Since the role of some of these genes in pathogenesis are still in dispute [36, 37], the annotations of experimental evidence for virulence have been provided to facilitate further investigation.