Pyrosequencing of 16S ribosomal RNA (rRNA) genes has become the gold standard in human microbiome studies. The routine task of taxonomic classification using 16S rRNA reads is commonly performed by the Ribosomal Database Project (RDP) II Classifier, a robust tool that relies on a set of well-characterized reference sequences. However, the RDP II Classifier may be unable to classify a significant part of the data set due to the absence of proper reference sequences. The taxonomic classification for some unclassified sequences might still be performed using BLAST searches against large and frequently updated nucleotide databases. Here we introduce TUIT (Taxonomic Unit Identification Tool)-an efficient open source and platform-independent application that can perform taxonomic classification on its own or can be used in combination with the RDP II Classifier to maximize the taxonomic identification rate. Using a set of simulated DNA sequences, we demonstrate that the algorithm performs taxonomic classification with high specificity for sequences as short as 125 base pairs. TUIT is applicable for 16S rRNA gene sequence classification; however, it is not restricted to 16S rRNA sequences. In addition, TUIT may be used as a complementary tool for effective taxonomic classification of nucleotide sequences generated by many current platforms, such as Roche 454 and Illumina. Stand-alone TUIT is available online at http://sourceforge.net/projects/tuit/.
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