parahaemolyticus of clinical and environmental origins. PCR methods have been applied FK506 nmr to the detection of bacterial pathogens for decades (Bej et al., 1999; Liu et

al., 2004a, 2005; Bauer & Rorvik, 2007; Kim et al., 2008a). The specificity of target sequences is crucial for their accurate identification. Specific genes or universal genes, including toxin genes and 16S rRNA gene, have been used as target markers for PCR assays (Martinez-Picado et al., 1994; Bej et al., 1999). Unfortunately, there is often significant nucleotide sequence similarity among toxin genes in bacterial species, especially within the same genus, and this sequence similarity has prevented these toxin genes from being useful targets for species-specific identification of bacterial pathogens (Chizhikov et al., 2001). The 16S rRNA gene sequences among the Vibrionaceae family showed >90% nucleotide sequence similarity when www.selleckchem.com/products/LBH-589.html analyzing this gene of 35 Vibrio strains (Urakawa et al., 1997). It seems that the high degree of sequence identity does not allow reliable discrimination of specific strains using PCR methods. Computational genomics has led the way to efficient and customized mining of genomes for species-specific nucleotide sequences. The blast program, a frequently used tool for nucleotide sequence

comparisons, has been applied to identify specific targets for the detection and identification of bacterial pathogens (Oggioni & Pozzi, 2001; Kim et al., 2006, 2008b). To mine targets with a high level of specificity, we identified 23 V. parahaemolyticus-specific candidate CDSs by standalone blast searching against the local database. Among the 23 V. parahaemolyticus-specific candidate CDSs, seven were designated hypothetical proteins, 14 were identified as putative genes and two were characterized by their function. Revealing the specificity of CDSs might be helpful in understanding the metabolic behaviors unique to V. parahaemolyticus. The specificity in silico is largely determined

Olopatadine by the screening criteria. If blastn searching of a query sequence returns a best-match sequence with the lowest e-value ≥0.001, the query sequence is considered to share little or no sequence similarity to any nucleotide sequence in the database, and, for our purposes, should be considered a specific sequence target (LaGier & Threadgill, 2008). Here, we chose the lowest e-value ≥0.1 as a standard to select V. parahaemolyticus-specific CDSs. In general, the process of identifying specific sequences will be made more reliable by the addition of more bacterial genomes to the database used for blast comparison. In this study, genome sequences of 811 non-V. parahaemolyticus bacteria proved to be sufficient for identifying V. parahaemolyticus-specific CDSs.