title: FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries.
abstract: BACKGROUND
  High-throughput sequencing makes it possible to rapidly obtain thousands of 16S rDNA sequences from environmental samples. Bioinformatic tools for the analyses of large 16S rDNA sequence databases are needed to comprehensively describe and compare these datasets.
  
  
  RESULTS
  FastGroupII is a web-based bioinformatics platform to dereplicate large 16S rDNA libraries. FastGroupII provides users with the option of four different dereplication methods, performs rarefaction analysis, and automatically calculates the Shannon-Wiener Index and Chao1. FastGroupII was tested on a set of 16S rDNA sequences from coral-associated Bacteria. The different grouping algorithms produced similar, but not identical, results. This suggests that 16S rDNA datasets need to be analyzed in multiple ways when being used for community ecology studies.
  
  
  CONCLUSIONS
  FastGroupII is an effective bioinformatics tool for the trimming and dereplication of 16S rDNA sequences. Several standard diversity indices are calculated, and the raw sequences are prepared for downstream analyses.
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA, USA. yyu@rohan.sdsu.edu
authors.forename: Yanan
authors.initials: Y
authors.lastname: Yu
authors.forename: Mya
authors.initials: M
authors.lastname: Breitbart
authors.forename: Pat
authors.initials: P
authors.lastname: McNairnie
authors.forename: Forest
authors.initials: F
authors.lastname: Rohwer
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D004269:DNA, Bacterial / Q000235:genetics*; D030561:Databases, Nucleic Acid; D015723:Gene Library; D020407:Internet; D009862:Online Systems; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S