I am analysing 454 pyrosequencing data for the identification of bacterial diversity by 16S rRNA gene sequencing. I have used RDP classifier for taxonomic assignment and now I want to cross verify it with the NCBI database.
please suggest me about the process so that I can analyse the classifier results in NCBI
The RDP classifier only for taxonomic assignment under and above genus level but not for species identification.
Surjit, you can use the NCBI blast results as reference sequences to build a phylogenetic tree with your query sequences. One way to work with short sequences is to use the Evolutionary Placement Algorithm (EPA) method to place your query seqeunces on your reference tree (See RaxML). Maybe for your tree, you can work only with your dominant sequences or OTUs or indicator OTUs. Another suggestion, you can also compare your results using another database, e.g. Greengenes
What platform are you using to process your sequence dataset? In QIIME, you can check BLAST and RDP Classifier with great ease. You just have to set it up that BLAST and RDP are both available for use.