The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries
Open accessAbstract
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. Conclusion: 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.
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Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
Woese, C. R., Kandler, O., & Wheelis, M. L. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.12.4576 · Cited by 6,128
Diversity and distribution of coral-associated bacteria
Rohwer, F., Seguritan, V, Azam, F., & Knowlton, N. (2002) · Marine Ecology Progress Series · doi:10.3354/meps243001 · Cited by 1,337
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UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context
Lozupone, C., Hamady, M., & Knight, R. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-371 · Cited by 1,453
Jones, R. T., Robeson, M. S., Lauber, C. L., Hamady, M., Knight, R., & Fierer, N. (2009) · The ISME Journal · doi:10.1038/ismej.2008.127 · Cited by 1,230
Oulas, A., Pavloudi, C., Polymenakou, P., Pavlopoulos, G. A., Papanikolaou, N., Kotoulas, G., Arvanitidis, C., & Iliopoulos, L. (2015) · Bioinformatics and Biology Insights · doi:10.4137/bbi.s12462 · Cited by 416
Middelbos, I. S., Vester Boler, B. M., Qu, A., White, B. A., Swanson, K. S., & Fahey, G. C. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009768 · Cited by 317
Bacterial Succession on the Leaf Surface: A Novel System for Studying Successional Dynamics
Redford, A. J., & Fierer, N. (2009) · Microbial Ecology · doi:10.1007/s00248-009-9495-y · Cited by 261
Metadata
- Authors
- Yu, Y., Breitbart, M., McNairnie, P., & Rohwer, F.
- Venue
- BMC Bioinformatics
- Published
- 2006-02-07
- Volume
- 7
- Issue
- 1
- Pages
- 57-57
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W1551834832
- Cited by
- 213
- References
- 2
- FWCI
- 6.02
- Type
- journal article
- Language
- en
- Open access
- gold
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