RDP_FrameBot

RDP FrameBot is a frameshift correction and nearest neighbor classification tool for use with high-throughput amplicon sequencing. It uses a dynamic programming algorithm to align each query DNA sequence against a set of target protein sequences, produces frameshift-corrected protein and DNA sequences and an optimal global or local protein alignment. It also helps filter out non-target reads. The online version of FrameBot is available on http://fungene.cme.msu.edu/FunGenePipeline, tutorial http://rdp.cme.msu.edu/tutorials/framebot/RDPtutorial_FRAMEBOT.html.

Updates: FrameBot now uses a kmer pre-filtering heuristic for no-metric-search. This pre-filtering may increase the speed by one to two orders of magnitude.

CITATION:
Wang, Q., Quensen, J. F., Fish, J. A., Lee, T. K., Sun, Y., Tiedje, J. M., and Cole, J. R. 2013. Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool. mBio 4:e00592-13.