Besides demonstrating the success of the CIBSI 2.0 program, the work involved in developing the algorithm allowed insight into the importance of proper ProSeq selection. The RPM v.1 was the first resequencing array designed specifically for multiple pathogen detection using database similarity searching and served as a prototype for this application. We have demonstrated that a single ProSeq with as few as 100 bp, when designed correctly, can be sufficient to unambiguously identify an organism. However, it is clearly indicated that several longer ProSeqs provide better confirmation and more detailed information of a pathogen. Although the algorithm provides accuracy equivalent to manual analysis for determinations of individual ProSeqs, the current algorithm is only partially successful in integrating information from multiple ProSeqs. The emphasis of the design to this point has been on capabilities that are generally applicable to any pathogen. We are incorporating these insights in our newer more comprehensive resequencing array designs. Improving on level of detail reported in pathogen determination Task(III) will require more information about an individual pathogen and may have to be developed for each specific pathogen or class of pathogens. This information is also required for the algorithm to identify which differences between a sample and database entries represent significant mutations. Future work will involve improving the use of the current taxonomic database or potentially developing a new relational database that is specific to our needs and then incorporating more specific information of target pathogens. The hierarchal design of the data analysis makes it easy to incorporate analysis that build upon the analysis already performed.