The CIBSI 2.0 program implemented in Perl described in this study handled a hierarchy of three tasks ( Figure 1 ): (I) Pro-Seq identification; (II) ProSeq grouping; and (III) pathogen determination. The most developed and important portion of the algorithm deals with ProSeq identification Task(I) and is handled in three important subtasks: initial filtering of individual HybSeqs into SubSeqs suitable for sequence similarity comparisons ( Figure 2 ), database querying of individual SubSeqs ( Figure 3 ) and taxonomic comparison of BLAST returns for each SubSeq (Figure 4 ). The NCBI BLAST and taxonomy databases were used for the queries and images were obtained on February 7, 2006. For the ProSeq grouping Task(II), ProSeqs were compared to determine if they supported the same identified organism. In the pathogen determination Task(III), detected organisms were compared to the list of target pathogens the assay was designed for in order to determine if any were positively detected or were possibly related close genetic near neighbors. The level of discrimination that a particular sample supported was automatically determined.