NBC update: The addition of viral and fungal databases to the Naïve Bayes classification tool

BMC Research Notes

Volumn 5, Issue , 2012, Pages

  Rosen, Gail L ^a   Lim, Tze ^b  

^a Drexel University   (United States)

^b DREXEL UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84856363643     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-5-81     Document Type: Article

References (17)

1. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. Baldrian P, et al. ISME J 2011 6 248 258 21776033
2. Viral metagenomics. Edwards RA, Rohwer F, Nat Rev Microbiol 2005 3 504 510 10.1038/nrmicro1163 15886693 (Pubitemid 40716177)
3. Potential bias of fungal 18S rDNA and internal transcribed spacer polymerase chain reaction primers for estimating fungal biodiversity in soil. Andersson IC, Campbell CD, Prosser JI, Environ Microbiol 2003 5 36 47 10.1046/j.1462-2920.2003.00383.x 12542711 (Pubitemid 36345744)
4. Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals. Ghannoum M, Jurevic R, Mukherjee P, Cui F, Sikaroodi M, Naqvi A, Gillevet P, PLoS Pathogens 2010 6
5. Massively parallel 454-sequencing of Quercus spp. ectomycorrhizosphere indicates differences in fungal community composition richness, and diversity among urban and rural environments. Jumpponen A, Jones K, Mattox J, Yeage C, Mol Ecol 2010 19 s1 41 53 20331769
6. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. Meyer F, et al. BMC Bioinformatics 2008 9 386 http://metagenomics.nmpdr.org/
7. A software pipeline for processing and identification of fungal ITS sequences. Nilson RH, Bok G, Ryberg M, Kristiansson E, Hallenberg N, Source Code Biol Med 2009 4
8. Taylor DL, Houston S, Methods in molecular biology, volume 722 of fungal genomics Hatfield, UK: Wiley and Sons, Inc. 2011
9. Naive Bayes Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Wang Q, Garrity G, Tiedje JM, Cole JR, Appl Environ Microbiol 2007 73 16 5261 5267 10.1128/AEM.00062-07 17586664 (Pubitemid 47326658)
10. NBC: The Naive Bayes Classification Tool Webserver for taxonomic classification of metagenomic reads. Rosen GL, Reichenberger E, Rosenfeld A, Bioinformatics 2011 27 127 129 10.1093/bioinformatics/btq619 21062764
11. Metagenome fragment classification using N-mer frequency profiles. Rosen GL, Garbarine EM, Caseiro DA, Polikar R, Sokhansanj BA, Advances Bioinformatics 2008 2008 Article ID 205969
12. An Empirical Study of Smoothing Techniques for Language Modeling. Chen SF, Goodman JT, Proceedings of the 34th Annual Meeting of the Association for Computational Linguistics 1996 310 318
13. Repetitive-Sequence-Based PCR Using the DiversiLab System for Identification of Aspergillus Species. Hansen D, et al. J Clin Microbiol 2008 46 5 1835 1839 10.1128/JCM.00956-07 18367576 (Pubitemid 351657237)
14. Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Amend AS, Seifert KA, Samson R, Bruns TD, Proc Natl Acad Sci USA 2010 107 13748 13753 10.1073/pnas.1000454107 20616017
15. MetaSim - A sequencing simulator for genomics and metagenomics. Richter DC, et al. PLoS ONE 2008 doi:10.1371/journal.pone.0003373
16. Evolution of mammals and their gut microbes. Ley RE, et al. Science 2008 320 5883 1647 1651 10.1126/science.1155725 18497261 (Pubitemid 351931256)
17. Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Hamady M, Knight R, Genome Res 2009 19 7 1141 1152 10.1101/gr.085464.108 19383763