Purified Chlamydia pneumoniae nucleic acid samples with 10-1000 genome copies (via method in Lin et al., submitted for publication) were chosen to illustrate how pathogen detection and identification were done when multiple ProSeqs were targeted for the same pathogen. RPM v.1 has three highly conserved ProSeqs selected from the genes encoding for the major outer membrane proteins VD2 and VD4, and the DNA-directed RNA polymerase (rpoB) gene. The HybSeqs from the different samples differed only in the number of unique base calls as shown in Table 1 . The percentage of the ProSeq called varied from 80 to 100% except for one case at a concentration of 10 that had only 11% of the rpoB ProSeq producing unique base calls. Because the samples at this concentration are not reproducibly generating the same percentage of base calls, this is probably the detection limit of this ProSeq of the assay. Table 1 listed the determinations made for the SubSeq and at the end of each task for the various samples. The ProSeq from the different cases produced the same number of SubSeqs. These SubSeqs from different samples reported different bit scores for the same top ranked returns from BLAST. In fact VD2 and VD4 produced exactly the same results. The NCBI taxonomy database classified the returns into four distinct groups, which represented the C.pneumoniae taxonomic group and three child strain groups. AE001652, AE002167, AE017159 and BA000008 appeared in the returns of all the ProSeqs for each sample, since they represented database entries of completely sequenced genomes. One rpoB Sub-Seq produced for its organism uniqueness, SeqUniqu. All other SubSeqs were TaxAmbig as multiple returns from different taxonomic classes were returned. Since the VD2 and VD4 ProSeq each have a single SubSeq, Task(I) assigned the Pro-Seq the state of the SubSeq. For the rpoB ProSeq, the bit score of one SubSeq was large enough that the algorithm assigned that SubSeq's identification to the ProSeq. Task II of the algorithm grouped all three ProSeqs together since they all had the same identified organism and TaxAmbig was assigned. The result of Task(III) was positive for target pathogen C.pneumoniae and this decision was straightforward as all the ProSeqs agreed with each other and belonged to the same target pathogen taxonomic class. Although the rpoB ProSeq was SeqUniqu, this was not the final conclusion for Task(II) as the ProSeq that was SeqUniqu was not the child taxonomic group and other ProSeq were TaxAmbig. The three recognized strains scored the same, which indicated that the sequence selected for the ProSeqs was very conserved and would not allow discrimination between the strains. Influenza and Human Adenovirus (HAdV) were the only pathogens that had ProSeq selected that would permit detailed strain level discrimination as discussed in previous work (15, 16) . This previous work using manual analysis found that the microarray results were in excellent agreement with the conventional sequencing results for clinical samples. A few of the results of running the CIBSI 2.0 program using the updated NCBI database on the raw microarray results are presented in Table 2 (the results for all samples used in the previous work are presented in Supplementary Table A) . The identified organisms were not identical to the original findings due to the difference in database used and because all ProSeqs were considered rather than only the Flu A and B hemagglutinin. In fact, the conventional sequencing results that were submitted to NCBI from that work were found for every sample to be among the returns with the best score for the hemagglutinin ProSeq (Supplementary Table B ). It should be noted that the previous work based its analysis upon only the results of the hemagglutinin ProSeq. For 8 of 13 Influenza A and 3 of 12 Influenza B cases, the results of ProSeq identification Task(I) and ProSeq grouping Task(II) found that the conventional sequencing was the single best return for the hemagglutinin ProSeq. Owing to the large number of isolate sequences in the database for the hemagglutinin gene it was not surprising that in some cases a single unique entry was not found. In each of the remaining five Influenza A samples, the other sequences returned differed by <0.2% from the conventional sequence. The fewer samples with unique isolate identifications for Influenza B were due to an older reference sequence used for the ProSeq, which allowed less Note: Within a row the first listing of a specific strain was followed by a two-letter abbreviation used in the remaining columns of that row. hybridization to occur (18) . This also meant that when multiple sequences were returned for a sample they represented greater genetic variation, up to 2%. As a result of the current method of making pathogen determination Task(III) level identification, the final organism reported was less specific (H3N2 or Flu B) for every sample than what was reported as possible in ProSeq grouping Task(II). For HAdV samples, the algorithm also reproduced the finer scale discriminations that had been made previously by manual methods (data not shown).