We next sought to demonstrate how a library of inferred phylogenies would be useful in making genome-scale predictions of genomic features that indirectly depend on local evolutionary histories.
Genomic conservation and local synteny between the human and zebrafish genomes make genome-scale and epigenetic analysis of these mutations (by microarray, chromatin immunoprecipitation sequencing, and RNA sequencing procedures) powerful methods for translational research and medical discovery.
Recent advances in high-thoughput DNA sequencing have made genome-scale analyses of genomes of extinct organisms possible.
Using GolgiP, we have made genome-scale predictions of Golgi-resident proteins in 18 plant genomes, and have made the preliminary analysis of the predicted data.
The tools listed can be replaced or supplemented by other tools (recently reviewed in [ 49, 50]) that are better suited to the organism of interest or yield improved accuracy, recognizing that some may require local installation of software to make genome-scale analyses feasible.
Moreover, we give our thoughts on the future of RNAi screening as a tool to enhance OVT and describe recent technical improvements that are poised to make genome-scale RNAi experiments more sensitive, less noisy, more applicable in vivo, and more easily validated in clinically relevant animal models.
DNA microarray technology has been leveraged to make genome-scale measurements across multiple layers of cellular molecules, e.g. gene expression (Schena et al., 1995), DNA copy number (Pinkel et al., 1998; Pollack et al., 1999), protein expression (Haab et al., 2001) and microRNA expression (Calin et al., 2004), among others.
The various attempts that have been made to draw genome-scale metabolic networks are confronted with two shortcomings: 1- they do not use contextual information which leads to dense, hard to interpret drawings, 2- they impose to fit to very constrained standards, which implies, in particular, duplicating nodes making topological analysis considerably more difficult.
However, to the best of our knowledge, attempts have yet to be made to establish genome-scale relationships between DNA curvature, CpG islands, tandem repeats and centromeric regions of any organism.
We have confirmed here that our strategy performs reasonably well at recovering known prions from large datasets of protein sequences, which makes it very appropriate to make predictions at genome scale.
