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The Carbohydrate-Active Enzyme (CAZy) database provides a rich set of manually annotated enzymes that degrade, modify, or create glycosidic bonds. Despite rich and invaluable information stored in the database, software tools utilizing this information for annotation of newly sequenced genomes by CAZy families are limited. We have employed two annotation(More)
Summary form only given. We highlight a fruitful interplay between biology and computation. The sequencing of complete genomes from multiple organisms has revealed that most differences in organism complexity are due to elements of gene regulation that reside in the non protein coding portions of genes. Both within and between species, transcription factor(More)
The development of computing systems with large numbers of processors has been motivated primarily by the need to solve large, complex problems more quickly than is possible with uniprocessor systems. Traditionally, multiprocessor systems have been uniprogrammed, i.e., dedicated to the execution of a single set of related processes, since this approach(More)
Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now(More)
Shewanellae are facultative gamma-proteobacteria whose remarkable respiratory versatility has resulted in interest in their utility for bioremediation of heavy metals and radionuclides and for energy generation in microbial fuel cells. Extensive experimental efforts over the last several years and the availability of 21 sequenced Shewanella genomes made it(More)