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Since the emergence of studies based on conservation in the noncoding regions, numerous findings have been made on conserved noncoding sequences (CNSs) in animals (Bejerano et al. 2004; Sandelin et al. 2004; Vavouri et al. 2007; Lee et al. 2010), plants (Kaplinsky et al. 2002; Guo and Moose 2003; Inada et al. 2003; Kritsas et al. 2012), and even bacteria (Marchais et al. 2009).
In this paper, the second one in the series beginning with [D. Mao, Towards front tracking based on conservation in two space dimensions, SIAM J. Sci. Comput. 22 (1) (2000) 113–151], we study another important feature of our 2D conservative front-tracking method, i.e. discontinuity curves in two space dimensions are tracked in a 1D capturing fashion.
PicTar has target prediction information for human miRNAs based on conservation in mammals (human, chimpanzee, mouse, rat, dog) [30].
Thus, it is simply not possible to assign the correct orthologous relationships by Blast searches, but syntenic position information can reveal which are orthologs based on conservation in the flanking genes [53].
Both datasets were based on conservation in mammals.
For PicTar, the result based on conservation in human, chimp, mouse, and rat was chosen.
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Conserved residues are shaded by different intensities based on conservation level in the alignment.
In this study, several theoretical models based on conservation equations in the system are used to evaluate the characteristics of LHPs.
It is important to note that these predictions are based on conservation of the site in multiple species and availability of the site in folded RNA.
The PromH scheme identifies promoters based on conservation of regulatory features in pairs of human/mouse orthologous genes.
However, the clustering analysis can also falsely lump non-identical members of gene families into the same contig based on conservation of sequence similarity in the coding region.
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