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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.
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.
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.
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.
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.
The human genome contains on the order of 20,000 genes which work in concert to produce roughly 1,000,000 distinct proteins. This is due to alternative splicing, and also because cells make important changes to proteins through posttranslational modification after they first construct them, so a given gene serves as the basis for many possible versions of a particular protein.
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Care should also be taken to avoid situations in which the species from which the sequences were taken are distantly related, but the gene encoded by the sequences is highly conserved across lineages. Horizontal gene transfer, especially between otherwise divergent bacteria, can also confound outgroup usage.