The probes are designed to have sequences complementary to segments of one or more target organism genomes.
The first target sequence has fewer base pairs involved in RNA secondary structure loops, allowing it to bind more with target genome, while the rest two both have 9 base pairs in loops.
The category I contains the highest number of global regulons (CcpA, Rex) and mid-size regulons that control 3 or more target operons per genome (AdcR, ArgR, CtsR, GlnR, HrcA, MalR, MtaR, PerR and PurR).
Mappable ratio is the percentage of unique PETs that have one or more target locations in the genome.
When fused to the VP64 activation domain and delivered to human cells by retrovirus, we found that each protein could find one or more targets in the genome and regulate adjacent genes.
Some contigs have significant association with two or more positions on a target genome.
In conclusion, the choice of the target genome region, more than the technology, is crucial for HCV genotyping/subtyping.
In cases where these initial queries failed to recover a candidate orthologue, query sequences from a taxon more closely related to the target genome (based on relationships from [ 19]) were used for further searching, should such a clear orthologue query be available, derived either from this survey or from annotated databases.
When more than one protein in a target genome meets these conditions with respect to the same S. cerevisiae protein we calculate an orthology score function, F. The protein with the highest F-score function is considered to be the most likely ortholog with respect to the S. cerevisiae protein, while the remaining proteins are flagged as in-paralogs of that ortholog.
