From reads of Sb2 (BTx430), 70 fragments comprising more than 35 kb of DNA and showing the highest density of candidate SNPs were selected.
Thus the analysis of retained introns in human cDNA, exons skipped due to mutations in splice sites and exons with cryptic sites produced results consistent with the intron definition mechanism of splicing of short introns, co-transcriptional splicing, dependence of splicing efficiency on the splice site strength and the density of candidate exonic splicing enhancers and silencers.
Several maps have been made for the zebrafish genome [ 4- 7], including a low density map of 2,035 SNPs and 178 insertion/deletion (indel) events [ 3], a high density map of candidate SNPS [ 8], dinucleotide microsatellites [ 9], and mutant loci [ 10].
Sulaiman et al. have now investigated epigenetic mechanisms involved in primary hyperparathyroidism by quantifying CpG island promoter methylation density of several candidate genes in parathyroid tumors and normal parathyroid references.
Array-based genotyping technologies that have enabled GWAS also permit flexibility in choosing the scope and density of SNPs for candidate gene studies.
The high density of plausible functional candidate genes makes it difficult to ascertain if the QTL is the product of a single gene with one large effect, or the combined effect of several genes in close proximity each with a small effect.
As shown in Fig. 6, with the increase of anchor node's density, the number of candidate samples in RMCL and RMCL grows remarkably.
However, when hot-spot areas other than the dominant one show a significantly lower density of immunopositive nuclei, the candidates from dominant region will still be selected first.
We believe it is counter-intuitive to consider genomic intervals with an extremely low density of SNVs as likely candidates for having experienced (or still experiencing) positive selection; low SNV density seems more indicative of negative selection.
As pointed out in Section 1, this filtering may lead to a loss of power in isoform detection because it disregards the read density information when constructing the set of candidates.
