An initial filtering algorithm, REPI, was developed previously (16) and the general concepts with revisions were incorporated into the current (automated detection) algorithm used in the CIBSI 2.0 program. Filtering and subsequence selection were used to remove potential biasing caused by reference sequence choice and by other sources (i.e. primers). When PCR amplification was used, microarrays were hybridized in the presence of only primers to determine locations where they resulted in hybridization. Any portions of the ProSeqs that hybridized with the primers were masked as N calls so that the HybSeq did not contain biased information. Normally the primers are designed to be outside the Pro-Seq region to minimize the interference caused by primers, and so minimize the bases to be masked. There is still the chance that some bases require masking because with the large number of primers used in the multiplex, short stretches of a ProSeq not corresponding to primer locations may still hybridize with the primers. Such regions could be removed from the reference sequences and so not appear on the microarray. However, determining such locations are a difficult and time-consuming task that for most cases is not worth the effort. The first subtask of ProSeq identification Task(I) is noted in Figure 1 and shown schematically in detail in Figure 2 . This subtask uses a procedure to examine a Hyb-Seq to find the longest possible subsequence of base calls (SubSeq) that can be submitted as a query to BLAST.