title: MycoBASE: expanding the functional annotation coverage of mycobacterial genomes.
abstract: BACKGROUND
  Central to most omic scale experiments is the interpretation and examination of resulting gene lists corresponding to differentially expressed, regulated, or observed gene or protein sets. Complicating interpretation is a lack of functional annotation assigned to a large percentage of many microbial genomes. This is particularly noticeable in mycobacterial genomes, which are significantly divergent from many of the microbial model species used for gene and protein functional characterization, but which are extremely important clinically. Mycobacterial species, ranging from M. tuberculosis to M. abscessus, are responsible for deadly infectious diseases that kill over 1.5 million people each year across the world. A better understanding of the coding capacity of mycobacterial genomes is therefore necessary to shed increasing light on putative mechanisms of virulence, pathogenesis, and functional adaptations.
  
  
  METHODS
  Here we describe the improved functional annotation coverage of 11 important mycobacterial genomes, many involved in human diseases including tuberculosis, leprosy, and nontuberculous mycobacterial (NTM) infections. Of the 11 mycobacterial genomes, we provide 9899 new functional annotations, compared to NCBI and TBDB annotations, for genes previously characterized as genes of unknown function, hypothetical, and hypothetical conserved proteins. Functional annotations are available at our newly developed web resource MycoBASE (Mycobacterial Annotation Server) at strong.ucdenver.edu/mycobase.
  
  
  CONCLUSIONS
  Improved annotations allow for better understanding and interpretation of genomic and transcriptomic experiments, including analyzing the functional implications of insertions, deletions, and mutations, inferring the function of understudied genes, and determining functional changes resulting from differential expression studies. MycoBASE provides a valuable resource for mycobacterial researchers, through improved and searchable functional annotations and functional enrichment strategies. MycoBASE will be continually supported and updated to include new genomes, enabling a powerful resource to aid the quest to better understand these important pathogenic and environmental species.
authors.affiliation: Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA. benjamin.garcia@ucdenver.edu.|Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA. benjamin.garcia@ucdenver.edu.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Garcia
authors.affiliation: Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.|Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.
authors.forename: Gargi
authors.initials: G
authors.lastname: Datta
authors.affiliation: Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.
authors.forename: Rebecca M
authors.initials: RM
authors.lastname: Davidson
authors.affiliation: Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.|Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Strong
mesh_terms: D058893:DNA Barcoding, Taxonomic; D030541:Databases, Genetic; D063990:Gene Ontology; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D058977:Molecular Sequence Annotation; D009161:Mycobacterium / Q000145:classification / Q000235:genetics*; D012984:Software; D064878:Web Browser