how to determin the taxonomy

Commands in mothur
1

hi Pat:

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 !
best wishes.

ling

2

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.

ling

3

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 ]
4

thanks~

I will try!