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Chromosome data continue to be of interest, especially in studies of hybrids in which multiple genomes are combined or genomes are duplicated.
Methods for motif discovery, for CRM prediction, and for the use of multiple genomes are compared through leave-one-out cross-validation (LOOCV) (see Figure 1).
Drosophila is ideally suited for such an approach not only because multiple genomes are now available, but also because a few regulatory networks, such as the segmentation network, have been well-established in vivo resulting in several deeply understood TF-TG relations.
If multiple genomes are analyzed together, the weight populations can be merged.
The application of SPR Opt is illustrated for two viruses for which multiple genomes are publicly available.
Furthermore, analysis methods based on multiple genomes are essential to properly evaluate the function and meaning of personal genome variants.
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Motivation: Identifying orthologous genes in multiple genomes is a fundamental task in comparative genomics.
Multiple genomes were analyzed in a comparative population genomic analysis including Z. tritici, Z. pseudotritici, and Z. ardabiliae to further assess signatures of positive selection and the speciation history of the three species (Stukenbrock et al. 2011).
Comparing multiple genomes is key for stopping S. pneumoniae, because 92 strains infect humans--and researchers would like to protect against them all.
Second, the availability of multiple genomes is, in general, extremely useful for genome-wide TG prediction.
The impact is multiplied when comparison of content and function among multiple genomes is the goal.
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