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As mentioned earlier, one of the key challenges in a comparative genomics method is reducing the dependence of the method on the reference genome set used.
For each genome set, 1000 new training and validation sets were generated from the original training set using the bagging method.
The result of annotation was then used to identify statistically significantly enriched pathways, diseases and GO terms using protein-coding genes from the whole human genome set (20,192 genes) as background.
Tab separated (txt) files containing Accession IDs and symbols derived from MEEBO genome set and the normalized expression ratios were then uploaded to Ingenuity Pathways Analysis.
Custom cDNA slides were spotted with Oligator "MEEBO" mouse genome set with 38,467 cDNA probes (Illumina, Inc., San Diego, CA), which allows interrogation of 25,000 genes.
RGPFinder searches for synteny breaks between a reference genome and a set of closely related bacteria, named the Bacterial genome set.
There are 7 chips in a full genome set and approximately 3,200,000 probe sets per chip (PM probes only).
Eukaryotic NEPs from the genome set have several dicysteines.
Categories (i) and (ii) are found in both Swiss-Prot and the genome set while category (iii) is found only in the genome set.
Several of the NEPs in the genome set also have cysteine cysteine dipeptides (Table 4).
For the genome set we see other dominant characters, "zinc finger" and "metal".
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