Comparative genomics, analyzing variation among individual genomes, is an area of intense investigation. DNA sequencing is usually employed to look for polymorphisms and mutations. Pyrosequencing, a real-time DNA sequencing method, is emerging as a popular platform for comparative genomics. Here we review the use of this technology for mutation scanning, polymorphism discovery and chemical hapl...

Background. The VIMSS Computational Core group is tasked with data management, statistical data analysis, modeling, and comparative and evolutionary genomics for the larger VIMSS effort. We have matured many of our analyses and VIMSS data into our flagship comparative functional microbial genomics tool MicrobesOnline (http://microbesonline.org). We have used this framework to interpret the data...

Plants form the foundation for our global ecosystem and are essential for environmental and human health. With an increasing number of available plant genomes and tractable experimental systems, comparative and functional plant genomics research is greatly expanding our knowledge of the molecular basis of economically and nutritionally important traits in crop plants. Inferences drawn from comp...

Understanding gene regulation is a key step to investigating gene functions and their relationships. Many algorithms have been developed to discover transcription factor binding sites (TFBS); they are predominantly located in upstream regions of genes and contribute to transcription regulation if they are bound by a specific transcription factor. However, traditional methods focusing on finding...

Comparative Genomics has exploded in recent years and put the techniques of molecular evolution at centre stages in harvesting structural information from sequence data. Originally, sequences/genomes were obtained from a single species at a time, but as more genomes have been determined, it has become apparent that the true benefit of this enterprise lies in comparison between genomes both with...

With the sequences of so many organisms’ genomes finished and available for use, comparative genomics has become a rapidly growing scientific discipline. In the spring of 2007, we plan to use comparative genomics to study the 4 chromosome (the ‘dot’ chromosome) of Drosophila by comparing the sequence of the Drosophila mojavensis dot chromosome to the sequences of the Drosophila melanogaster and...

Background: Finding orthologous genes among multiple sequenced genomes is a primary step in comparative genomics studies. With the number of sequenced genomes increasing exponentially, comparative genomics becomes more powerful than ever for genomic analysis. However, the very large number of genomes in need of analysis makes conventional orthology prediction methods incapable of this task. Thu...

The multitude of bacterial genome sequences being determined has opened up a new field of research, that of comparative genomics. One role of bioinformatics is to assist biologists in the extraction of biological knowledge from this data flood. Software designed for the analysis and functional annotation of a single genome have, in consequence, evolved towards comparative genomics tools, bringi...

Although transcriptional regulation is fundamental to understanding bacterial physiology, the targets of most bacterial transcription factors are not known. Comparative genomics has been used to identify likely targets of some of these transcription factors, but these predictions typically lack experimental support. Here, we used mutant fitness data, which measures the importance of each gene f...

MOTIVATION Analysis of multiple genomes requires sophisticated tools that provide search, visualization, interactivity and data export. Comparative genomics datasets tend to be large and complex, making development of these tools difficult. In addition to scalability, comparative genomics tools must also provide user-friendly interfaces such that the research scientist can explore complex data ...