Secondary metabolite unique regions finder (SMURF) is a web-based tool [ 54] that finds secondary metabolite biosynthesis gene clusters and pathways in fungal genomes based on their genomic context and domain content.
For PCR primer design, the original (not bisulfite converted) DNA sequences flanking the predicted Alu insertion sites were extracted from the UCSC reference human genome, based on their genomic coordinates [ 48].
Next, all GIs residing in the same genome were compared with each other by calculating the average dinucleotide relative abundance difference, or genomic dissimilarity [ 20], after which we cluster all compositionally similar GIs per genome, based on their genomic dissimilarity values using δρ-Web and Compare_Islands [ 19, 25], respectively.
We then integrated the TSSs from the two datasets into one and clustered them based on their genomic locations.
These values allowed us to rate the contig sequences based on their genomic copy numbers and proportion in the genome, respectively.
The remaining 173,122 probes were annotated based on their genomic map positions relative to the B73 reference genome [21] and conservation in the Mo17 genome.
We therefore classified SNPs based on their genomic locations.
This approach resulted in the genome wide identification of 3067 transcription start sites (TSSs) that were further classified based on their genomic positions.
So the team came up with a mathematical technique for grouping tumors based on their genomic similarities.
Based on their genomic analysis, recA and polA exhibit signs of coevolution in ionizing radiation-resistant bacteria [9].
The cattle isolates were selected based on their genomic backgrounds as determined by multilocus enzyme electrophoresis (MLEE) and MLST (Table 1).
