from Luo et al (2011) in Microbial Population Genetics

The rapid accumulation of bacterial genome sequences has opened up a new field of research, that of comparative genomics. Interpretation of raw DNA sequence data involves the identification and annotation of genes, proteins, and regulatory and/or metabolic pathways. Therefore, there is a natural shift towards the creation of tools for viewing and manipulating data in a comparative genomics context. In addition, genome annotations need to be reprocessed on a regular basis to take into account the newly characterized functions of genes. Furthermore, large-scale functional analyses generate additional data that contribute to the interpretation of genomic data. These considerations are driving the research community to think about how to manage public collections of genomes in novel ways. One role of bioinformatics is to assist biologists in the extraction of biological knowledge from this flood of data. Consequently, software designed for the analyses and functional annotation of a single genome have evolved to tools for comparative genomics, detecting the relatively conserved information across many genomes simultaneously. Here we introduce several popular tools for bacterial genome annotation and comparative genomics.

Tags: Microbial Population Genetics | Population Genetics | Analytic Tools in Comparative Genomics | Comparative Genomics | Comparative Genomics Tools | Comparative Microbial Genomics | Population Genetic Patterns and Evolutionary Implications | Microbial genomics