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A consensus logo is a simplified variation of a sequence logo that can be embedded in text format. Like a sequence logo, a consensus logo is created from a collection of aligned protein or DNA/RNA sequences and conveys information about the conservation of each position of a sequence motif or sequence alignment [1] [4].
The score is greater than 0 if it is more likely to be a functional site than a random site, and less than 0 if it is more likely to be a random site than a functional site. [1] The sequence score can also be interpreted in a physical framework as the binding energy for that sequence.
In 1997, Matsuda, et al. devised a code they called the "three-dimensional chain code" for representing the protein structure as a string of letters. This encoding scheme reveals the similarity between the proteins much more clearly than the amino acid sequence (example from article): [ 12 ] The code encodes the torsion angles between alpha ...
[1] In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids (DNA and RNA) or proteins across species (orthologous sequences), or within a genome (paralogous sequences), or between donor and receptor taxa (xenologous sequences). Conservation indicates that a sequence has been maintained by natural selection.
[2] Any mutation allowing a mutated nucleotide in the core promoter sequence to look more like the consensus sequence is known as an up mutation. This kind of mutation will generally make the promoter stronger, and thus the RNA polymerase forms a tighter bind to the DNA it wishes to transcribe and transcription is up-regulated.
Each bar or space is 1, 2, 3 or 4 units wide, the sum of the widths of bars must be even (4, 6 or 8 units), the sum of the widths of the spaces must be odd (3, 5 or 7 units), and total 11 units per symbol. For instance, encoding the ASCII character "0" can be viewed as 10011101100, where a sequence of 1's is a bar and a sequence of 0's is a space.
Here's the whimsical story of how that iconic logo originated: In the early 1980s, Scott Nash, just out of design school, found himself on a flight to meet with executives from the nascent cable ...
[1] [2] It is a cloud-based data storage and analysis platform developed at the Centre for Biodiversity Genomics in Canada. It consists of four main modules, a data portal, an educational portal, a registry of BINs (putative species), and a data collection and analysis workbench which provides an online platform for analyzing DNA sequences. [2]