The next subtask of ProSeq identification Task(I) carried out was the determination of SubSeq() states and is shown in Figure 3 . The BLAST algorithm gives a ranking score which can be reported as accounting for the size of the database (expect value) or not (bit score). The full taxonomic classifications of every return for a SubSeq were retrieved from the NCBI taxonomy database obtained on February 7, 2006. Using the scores and taxonomy relationships it was possible to find a reduced number of returns that had the best match with the HybSeq. These results were summarized by identifying the taxonomic class to which all the returns belonged to, 'identified organism', and a parameter that indicated how they are related to each other, 'organism uniqueness'. A detailed description of the steps is contained in Supplementary Data. After each SubSeq was examined, the algorithm moved to the next subtask, which was to determine the identified organism of the ProSeq from the SubSeq (Figure 4 ). The subsequences from the same ProSeq were only allowed to support a single 'identified organism' determination. The procedure shown in Figure 4 demonstrates the decision method used to arrive at this determination (detailed description in Supplementary Data). After the subtask covered in Figure 4 was completed, the ProSeq identification Task(I) loop continued until all ProSeqs were examined. A list of ProSeqs that had detected organisms was built up in the Result1 array.