In this paper, we describe a new software expert system, Computer-Implemented Biological Sequence Identifier system 2.0 (CIBSI 2.0), that successfully uses resolved base sequence information from custom designed Affymetrix resequencing microarrays to provide a simple list of organisms that are detected. This algorithm addresses the most important shortcoming of previous methods by incorporating new features to completely automate pathogen identification. We have demonstrated the effectiveness of this algorithm for identification via several examples. The single program is capable of making correct decisions for all 26 pathogens contained on the Respiratory Pathogen Microarray v.1 (RPM v.1), whether detected alone or in combinations, with improved sensitivity. Although the program is currently applied to resequencing microarrays, the methodologies developed remain generally applicable. Only the first portion of the algorithm handles issues specific to microarrays while the remainder deals with sequences that are suitable for use as a query by the BLAST algorithm. In developing the general identification algorithm, we have identified and resolved issues specific to resequencing microarrays that complicate their use. Because the entire decision process for what is detected has been automated, it is straightforward to test whether the rules used to make identifications are rigorous and applicable to any pathogen. With this efficient program, resequencing based assays can provide a competitive method to test simultaneously for many possible pathogens, providing output that can be interpreted by a nonexpert.