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One way to visualize the similarity between two protein or nucleic acid sequences is to use a similarity matrix, known as a dot plot. These were introduced by Gibbs and McIntyre in 1970 [1] and are two-dimensional matrices that have the sequences of the proteins being compared along the vertical and horizontal axes.
A De Finetti diagram visualizing genotype frequencies as distances to triangle edges x (AA), y (Aa) and z (aa) in a ternary plot. The curved line are the Hardy–Weinberg equilibria. A Punnett square visualizing the genotype frequencies of a Hardy–Weinberg equilibrium as areas of a square. p (A) and q (a) are the allele frequencies.
A de Finetti diagram. The curved line is the expected Hardy–Weinberg frequency as a function of p.. A de Finetti diagram is a ternary plot used in population genetics.It is named after the Italian statistician Bruno de Finetti (1906–1985) and is used to graph the genotype frequencies of populations, where there are two alleles and the population is diploid.
Gene Set Association Analysis for RNA-Seq GSAASeq are computational methods that assess the differential expression of a pathway/gene set between two biological states based on sequence count data. GeneSCF a real-time based functional enrichment tool with support for multiple organisms.
Ab Initio gene prediction is an intrinsic method based on gene content and signal detection. Because of the inherent expense and difficulty in obtaining extrinsic evidence for many genes, it is also necessary to resort to ab initio gene finding, in which the genomic DNA sequence alone is systematically searched for certain tell-tale signs of protein-coding genes.
N50 statistic defines assembly quality in terms of contiguity.Given a set of contigs, the N50 is defined as the sequence length of the shortest contig at 50% of the total assembly length.
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An illustration of a Manhattan plot depicting several strongly associated risk loci. A Manhattan plot is a type of plot, usually used to display data with a large number of data-points, many of non-zero amplitude, and with a distribution of higher-magnitude values.