Two intergenic regions had useful polymorphisms for the design of classification probes to test on genomic DNA from other known isolates.
Genes corresponding to our classification probe-sets were identified in the published datasets.
For tissue classification, the probe set intensities of the 56 genes or an equivalent number of random probe sets of the 24 selected tissues were extracted from each of the three GEO datasets using the programs Microsoft Access and Excel.
It is clear from the GACK classification of probe absences (see Additional Files 4 and 5) that SCO6832 is largely intact/present, as of the 18 probes targeting this gene all but three are present/non-divergent, i.e. only the first probe targeting the 5' terminus and the two probes targeting the 3' terminus do not bind.
Using a conservative criterion for classification, discarding probes overlapping ncRNA genes and only considering neighboring probes, still results in the co-occupancy effect among the neighboring probes, suggesting that neither the high copy number of tRNAs nor of their associated Ty elements are responsible for the co-occupancy effect.
To test for this, we inspected spot intensities and performed a more finely-grained classification of probes.
Additional file 4 shows the degree of concordance between the platforms with respect to the classification of probes as amplifications, deletions or normal.
In the case of plasmid classification, labelled probes were generated by using DIG-labelled dUTP and primers repCF10-1/2 repCF10-1/2-1/2 for plandid repRE25-1/2 repRE25-1/2 (Additional fore 2: Table S2).
A total of 77 user-defined gene sets were generated from GeneSpring derived Gene Ontology annotations for various molecular classifications and probe sets of differentially expressed genes between days 3 and 15 of micromass culture (James et al., 2005).
Note that the detection thresholds used here are not optimized with respect to the number of concordant classifications of probes.
Together, the manual and automatic classification called 653 probe sets on the MOE430 2.0 GeneChip as NAT-detecting probe sets, which are listed in Additional file 1 annotated with the gene symbol and the result of manual and automated validation.
