PMID- 22293603
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20121002
LR  - 20211021
IS  - 1756-0500 (Electronic)
IS  - 1756-0500 (Linking)
VI  - 5
DP  - 2012 Jan 31
TI  - NBC update: The addition of viral and fungal databases to the Naive Bayes 
      classification tool.
PG  - 81
LID - 10.1186/1756-0500-5-81 [doi]
AB  - BACKGROUND: Classifying the fungal and viral content of a sample is an important 
      component of analyzing microbial communities in environmental media. Therefore, a 
      method to classify any fragment from these organisms' DNA should be implemented. 
      RESULTS: We update the naive Bayes classification (NBC) tool to classify reads 
      originating from viral and fungal organisms. NBC classifies a fungal dataset 
      similarly to Basic Local Alignment Search Tool (BLAST) and the Ribosomal Database 
      Project (RDP) classifier. We also show NBC's similarities and differences to RDP 
      on a fungal large subunit (LSU) ribosomal DNA dataset. For viruses in the 
      training database, strain classification accuracy is 98%, while for those reads 
      originating from sequences not in the database, the order-level accuracy is 78%, 
      where order indicates the taxonomic level in the tree of life. CONCLUSIONS: In 
      addition to being competitive to other classifiers available, NBC has the 
      potential to handle reads originating from any location in the genome. We 
      recommend using the Bacteria/Archaea, Fungal, and Virus databases separately due 
      to algorithmic biases towards long genomes. The tool is publicly available at: 
      http://nbc.ece.drexel.edu.
FAU - Rosen, Gail L
AU  - Rosen GL
AD  - Department of Electrical and Computer Engineering, Drexel University, 
      Philadelphia, PA, USA. gailr@ece.drexel.edu.
FAU - Lim, Tze Yee
AU  - Lim TY
LA  - eng
PT  - Journal Article
DEP - 20120131
PL  - England
TA  - BMC Res Notes
JT  - BMC research notes
JID - 101462768
PMC - PMC3284397
EDAT- 2012/02/02 06:00
MHDA- 2012/02/02 06:01
PMCR- 2012/01/31
CRDT- 2012/02/02 06:00
PHST- 2011/10/20 00:00 [received]
PHST- 2012/01/31 00:00 [accepted]
PHST- 2012/02/02 06:00 [entrez]
PHST- 2012/02/02 06:00 [pubmed]
PHST- 2012/02/02 06:01 [medline]
PHST- 2012/01/31 00:00 [pmc-release]
AID - 1756-0500-5-81 [pii]
AID - 10.1186/1756-0500-5-81 [doi]
PST - epublish
SO  - BMC Res Notes. 2012 Jan 31;5:81. doi: 10.1186/1756-0500-5-81.