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The larger the difference between entropies, the more conserved (longer) the haplotype that carries the minor variant, consistent with a recent selective sweep.
> -wrap-foot> UCEs are defined as nucleotide sequences that are absolutely conserved longer than 200 bp between orthologous regions of the human, rat and mouse.
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The question, however, remains whether gene number and structure of the complex is conserved during longer terms of evolution.
The human CNE-enhancers opted for this purpose is conserved over longer evolutionary distance, i.e. between human and teleost fish.
Several of the conclusions are quite different when viewed in the light of structure which is conserved over longer evolutionary time scales than sequence.
The fact that no pattern is coherently conserved for longer timescales is surprising considering the fact that 15% of the regulatory genes have conservation scores higher than 1.
The situation could be somewhat improved [ 7] if one compares proteins' three-dimensional structures which are conserved over longer evolutionary times.
Conserved regions longer then the average fragment length (450 bp) may introduce ambiguity in the assembly process due to a lack of direct evidence of sub-genomes phasing across the conserved region.
The same set of unigenes produced 647 significant hits (conserved region longer than 100 bp and similarity ≥ 80%) in a further BLASTN search against the GenBank EST database [ 32], indicating that similar transcripts were previously isolated.
Although there is a decrease in purifying selection immediately following duplication, which may lead to a higher d N/d S, there is also a general tendency for genes that are retained in duplicate to be more conserved over longer timescales, leading to a decreased d N/d S (Jordan et al. 2004).
However, the high rate of spurious occurrences of 6mers on a genome-wide analysis forces the majority of predictions algorithms to mainly focusing on conserved and/or longer seed matches (e.g.: 7-8mer seeds) to restrict the number of false positives.
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