Protein sequencingProtein sequencing is the practical process of determining the amino acid sequence of all or part of a protein or peptide. This may serve to identify the protein or characterize its post-translational modifications. Typically, partial sequencing of a protein provides sufficient information (one or more sequence tags) to identify it with reference to databases of protein sequences derived from the conceptual translation of genes. The two major direct methods of protein sequencing are mass spectrometry and Edman degradation using a protein sequenator (sequencer).
Consensus sequenceIn molecular biology and bioinformatics, the consensus sequence (or canonical sequence) is the calculated sequence of most frequent residues, either nucleotide or amino acid, found at each position in a sequence alignment. It represents the results of multiple sequence alignments in which related sequences are compared to each other and similar sequence motifs are calculated. Such information is important when considering sequence-dependent enzymes such as RNA polymerase.
Protein primary structureProtein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the laboratory. Protein primary structures can be directly sequenced, or inferred from DNA sequencess.
Viterbi algorithmThe Viterbi algorithm is a dynamic programming algorithm for obtaining the maximum a posteriori probability estimate of the most likely sequence of hidden states—called the Viterbi path—that results in a sequence of observed events, especially in the context of Markov information sources and hidden Markov models (HMM). The algorithm has found universal application in decoding the convolutional codes used in both CDMA and GSM digital cellular, dial-up modems, satellite, deep-space communications, and 802.
Protein superfamilyA protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology). Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similarity is evident. Sequence homology can then be deduced even if not apparent (due to low sequence similarity). Superfamilies typically contain several protein families which show sequence similarity within each family.
Dijkstra's algorithmDijkstra's algorithm (ˈdaɪkstrəz ) is an algorithm for finding the shortest paths between nodes in a weighted graph, which may represent, for example, road networks. It was conceived by computer scientist Edsger W. Dijkstra in 1956 and published three years later. The algorithm exists in many variants. Dijkstra's original algorithm found the shortest path between two given nodes, but a more common variant fixes a single node as the "source" node and finds shortest paths from the source to all other nodes in the graph, producing a shortest-path tree.
Evolutionary biologyEvolutionary biology is the subfield of biology that studies the evolutionary processes (natural selection, common descent, speciation) that produced the diversity of life on Earth. It is also defined as the study of the history of life forms on Earth. Evolution holds that all species are related and gradually change over generations. In a population, the genetic variations affect the phenotypes (physical characteristics) of an organism. These changes in the phenotypes will be an advantage to some organisms, which will then be passed onto their offspring.
Short linear motifIn molecular biology short linear motifs (SLiMs), linear motifs or minimotifs are short stretches of protein sequence that mediate protein–protein interaction. The first definition was given by Tim Hunt: "The sequences of many proteins contain short, conserved motifs that are involved in recognition and targeting activities, often separate from other functional properties of the molecule in which they occur. These motifs are linear, in the sense that three-dimensional organization is not required to bring distant segments of the molecule together to make the recognizable unit.
Threading (protein sequence)In molecular biology, protein threading, also known as fold recognition, is a method of protein modeling which is used to model those proteins which have the same fold as proteins of known structures, but do not have homologous proteins with known structure. It differs from the homology modeling method of structure prediction as it (protein threading) is used for proteins which do not have their homologous protein structures deposited in the Protein Data Bank (PDB), whereas homology modeling is used for those proteins which do.
Biological organisationBiological organisation is the organisation of complex biological structures and systems that define life using a reductionistic approach. The traditional hierarchy, as detailed below, extends from atoms to biospheres. The higher levels of this scheme are often referred to as an ecological organisation concept, or as the field, hierarchical ecology. Each level in the hierarchy represents an increase in organisational complexity, with each "object" being primarily composed of the previous level's basic unit.
Evolutionary computationIn computer science, evolutionary computation is a family of algorithms for global optimization inspired by biological evolution, and the subfield of artificial intelligence and soft computing studying these algorithms. In technical terms, they are a family of population-based trial and error problem solvers with a metaheuristic or stochastic optimization character. In evolutionary computation, an initial set of candidate solutions is generated and iteratively updated.
Single-nucleotide polymorphismIn genetics and bioinformatics, a single-nucleotide polymorphism (SNP snɪp; plural SNPs snɪps) is a germline substitution of a single nucleotide at a specific position in the genome that is present in a sufficiently large fraction of considered population (generally regarded as 1% or more). For example, a G nucleotide present at a specific location in a reference genome may be replaced by an A in a minority of individuals. The two possible nucleotide variations of this SNP – G or A – are called alleles.
