FunGene: the functional gene pipeline and repository

Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a…

• UD
  U.S. Department of Energy

  Awards: FC02-07ER64494, 07ER64494, DE-FC02-07ER64494, DE-FG02-99ER62848, FG02-99ER62848, DE-FG02-, DE-FG02
• UD
  U.S. Department of Agriculture

  Award: DE-FC02-07ER64494
• NI
  National Institutes of Health

  Awards: P42 ES004911, UH3 DK083993
• NI
  National Institute of Food and Agriculture

  Award: DE-FC02-07ER64494
• OO
  Office of Science

  Awards: DE-FC02-07ER64494, FC02-07ER64494