In bioinformatics and evolutionary biology, a substitution matrix describes the frequency at which a character in a nucleotide sequence or a protein sequence changes to other character states over evolutionary time. The information is often in the form of log odds of finding two specific character states aligned and depends on the assumed number of evolutionary changes or sequence dissimilarity between compared sequences. It is an application of a stochastic matrix. Substitution matrices are usually seen in the context of amino acid or DNA sequence alignments, where they are used to calculate similarity scores between the aligned sequences.
In the process of evolution, from one generation to the next the amino acid sequences of an organism's proteins are gradually altered through the action of DNA mutations. For example, the sequence
ALEIRYLRD
could mutate into the sequence
ALEINYLRD
in one step, and possibly
AQEINYQRD
over a longer period of evolutionary time. Each amino acid is more or less likely to mutate into various other amino acids. For instance, a hydrophilic residue such as arginine is more likely to be replaced by another hydrophilic residue such as glutamine, than it is to be mutated into a hydrophobic residue such as leucine. (Here, a residue refers to an amino acid stripped of a hydrogen and/or a hydroxyl group and inserted in the polymeric chain of a protein.) This is primarily due to redundancy in the genetic code, which translates similar codons into similar amino acids. Furthermore, mutating an amino acid to a residue with significantly different properties could affect the folding and/or activity of the protein. This type of disruptive substitution is likely to be removed from populations by the action of purifying selection because the substitution has a higher likelihood of rendering a protein nonfunctional.
If we have two amino acid sequences in front of us, we should be able to say something about how likely they are to be derived from a common ancestor, or homologous.
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A protein family is a group of evolutionarily related proteins. In many cases, a protein family has a corresponding gene family, in which each gene encodes a corresponding protein with a 1:1 relationship. The term "protein family" should not be confused with family as it is used in taxonomy. Proteins in a family descend from a common ancestor and typically have similar three-dimensional structures, functions, and significant sequence similarity.
Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa. For example, these techniques have been used to explore the family tree of hominid species and the relationships between specific genes shared by many types of organisms.
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.
We address the mining of sequential activity patterns from document logs given as word-time occurrences. We achieve this using topics that models both the cooccurrence and the temporal order in which words occur within a temporal window. Discovering such t ...
2010
,
The need for interfacing structural biology and biophysics to molecular evolution is being increasingly recognized. One part of the big problem is to understand how physics and chemistry shape the sequence space available to functional proteins, while sati ...
The LHCb experiment is designed to perform high-precision measurements of CP-violation and rare decays of B hadrons at the Large Hadron Collider. The Silicon Tracker (ST) is a silicon strip detector intended to precisely measure the particle trajectories p ...