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In the 15 years that have passed since then, many functional genomic studies using the S288c genome as a reference sequence have greatly enriched our knowledge of how yeast cells respond to and resist various environmental stresses [ 8- 16].
The entire genome sequence for C. elegans is available and many functional genomic approaches have been developed.
Global correlations between intragenic DNA methylation and specific histone modifications have been difficult to establish in other species in part because DNA methylation has many functional genomic targets (e.g. introns, exons, promoters, repeats, etc).
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With the completion of rice genome sequencing by the International Rice Genome Sequencing Project [ 1], the Beijing Genomics Institute (BGI) [ 2], and Syngenta [ 3], many rice functional genomic resources have become available, including whole genome sequences from ssp. japonica 'Nipponbare' and ssp.
EST sequencing projects have facilitated appropriate strategies for gene discovery [ 6], molecular markers identification [ 7, 8], and many other functional genomic developments and tools, e.g. microarray approaches [ 9- 11].
Additional analysis suggested many micSeqs are functional genomic elements involved in biological functions.
Although many of the functional genomic elements are protein-coding sequences, a large number of conserved sequences are probably regulatory elements with roles in modulating gene expression9,10.
Another study in zebrafish has shown that the up-to-date alignment techniques are unable to detect many of the functional genomic regions (McGaughey et al. 2008).
Although G4 structures have stability with higher temperature than that of canonical double helix structures, many functional regions in genomic sequences have not a few G-rich motifs [ 2], motivating us to investigate further the functional roles of G4 structures.
Despite a plethora of functional genomic efforts, the function of many genes in sequenced genomes remains unknown.
This approach will allow exploiting many of the already established functional genomic resources, like i.e. the large mutant collections, that are available for Arabidopsis.
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