I want to give the taxonomy of the query sequences, and I read the command “classify.seqs” with the wang method. Now I have some trouble.
I can’t understand the following description"This method also runs a bootstrapping algorithmn to find the confidence limit of the assignment by randomly choosing with replacement 1/8 of the kmers in the query and then finding the taxonomy." can you give me an example for it?
thank you !
hi Pat :
I have another request, now I need some reference papers for Phylotype analysis, can you help me ? give me one related paper or more?
thank you very much.
you can find citations for each command by running the function name with the citation key word in the parentheses…
mothur > classify.seqs(citation)
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-7. [ for Bayesian classifier ]
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402. [ for BLAST ]
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-72. [ for kmer ]