Sequence motif, the Glossary
In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule.[1]
Table of Contents
67 relations: Amino acid, Artificial bee colony algorithm, Bayesian inference, Bioinformatics, Biomolecular structure, BLAST (biotechnology), Cell (biology), Consensus sequence, Conserved sequence, Cuckoo search, Database, Dihedral angle, DNA, DNA binding site, DNA-binding domain, DNA-binding protein, Escherichia coli, Exon, Function (biology), GCM transcription factors, Gene, Genetic algorithm, Genetic code, Hidden Markov model, International Union of Pure and Applied Chemistry, IQ calmodulin-binding motif, Junk DNA, MaMF, Markov model, Markov random field, MochiView, Multiple EM for Motif Elicitation, N-linked glycosylation, Non-coding DNA, Nucleic acid, Nucleic acid sequence, Nucleotide, Operon, Particle swarm optimization, Pattern, Pfam, Phosphorylation, Phylogenetics, Planted motif search, Polymer backbone, Position weight matrix, PROSITE, Protein, Protein domain, Protein I-sites, ... Expand index (17 more) »
Amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups.
See Sequence motif and Amino acid
Artificial bee colony algorithm
In computer science and operations research, the artificial bee colony algorithm (ABC) is an optimization algorithm based on the intelligent foraging behaviour of honey bee swarm, proposed by Derviş Karaboğa (Erciyes University) in 2005.
See Sequence motif and Artificial bee colony algorithm
Bayesian inference
Bayesian inference is a method of statistical inference in which Bayes' theorem is used to update the probability for a hypothesis as more evidence or information becomes available.
See Sequence motif and Bayesian inference
Bioinformatics
Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex.
See Sequence motif and Bioinformatics
Biomolecular structure
Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function.
See Sequence motif and Biomolecular structure
BLAST (biotechnology)
In bioinformatics, BLAST (basic local alignment search tool) is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences.
See Sequence motif and BLAST (biotechnology)
Cell (biology)
The cell is the basic structural and functional unit of all forms of life.
See Sequence motif and Cell (biology)
Consensus sequence
In 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. Sequence motif and consensus sequence are bioinformatics.
See Sequence motif and Consensus sequence
Conserved sequence
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).
See Sequence motif and Conserved sequence
Cuckoo search
In operations research, cuckoo search is an optimization algorithm developed by Xin-She Yang and Suash Deb in 2009.
See Sequence motif and Cuckoo search
Database
In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and analyze the data.
See Sequence motif and Database
Dihedral angle
A dihedral angle is the angle between two intersecting planes or half-planes.
See Sequence motif and Dihedral angle
DNA
Deoxyribonucleic acid (DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix.
DNA binding site
DNA binding sites are a type of binding site found in DNA where other molecules may bind. Sequence motif and DNA binding site are bioinformatics.
See Sequence motif and DNA binding site
DNA-binding domain
A DNA-binding domain (DBD) is an independently folded protein domain that contains at least one structural motif that recognizes double- or single-stranded DNA.
See Sequence motif and DNA-binding domain
DNA-binding protein
DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA.
See Sequence motif and DNA-binding protein
Escherichia coli
Escherichia coliWells, J. C. (2000) Longman Pronunciation Dictionary.
See Sequence motif and Escherichia coli
Exon
An exon is any part of a gene that will form a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing.
Function (biology)
In evolutionary biology, function is the reason some object or process occurred in a system that evolved through natural selection.
See Sequence motif and Function (biology)
GCM transcription factors
In molecular biology, the GCM transcription factors are a family of proteins which contain a GCM motif.
See Sequence motif and GCM transcription factors
Gene
In biology, the word gene has two meanings.
Genetic algorithm
In computer science and operations research, a genetic algorithm (GA) is a metaheuristic inspired by the process of natural selection that belongs to the larger class of evolutionary algorithms (EA).
See Sequence motif and Genetic algorithm
Genetic code
The genetic code is the set of rules used by living cells to translate information encoded within genetic material (DNA or RNA sequences of nucleotide triplets, or codons) into proteins.
See Sequence motif and Genetic code
A hidden Markov model (HMM) is a Markov model in which the observations are dependent on a latent (or "hidden") Markov process (referred to as X). An HMM requires that there be an observable process Y whose outcomes depend on the outcomes of X in a known way. Sequence motif and hidden Markov model are bioinformatics.
See Sequence motif and Hidden Markov model
International Union of Pure and Applied Chemistry
The International Union of Pure and Applied Chemistry (IUPAC) is an international federation of National Adhering Organizations working for the advancement of the chemical sciences, especially by developing nomenclature and terminology.
See Sequence motif and International Union of Pure and Applied Chemistry
IQ calmodulin-binding motif
The IQ calmodulin-binding motif is an amino acid sequence motif containing the following sequence.
See Sequence motif and IQ calmodulin-binding motif
Junk DNA
Junk DNA (non-functional DNA) is a controversial term referring to types of Non-Coding DNA that is considered obsolete by many scientists.
See Sequence motif and Junk DNA
MaMF
MaMF, or Mammalian Motif Finder, is an algorithm for identifying motifs to which transcription factors bind. Sequence motif and MaMF are bioinformatics.
Markov model
In probability theory, a Markov model is a stochastic model used to model pseudo-randomly changing systems.
See Sequence motif and Markov model
Markov random field
In the domain of physics and probability, a Markov random field (MRF), Markov network or undirected graphical model is a set of random variables having a Markov property described by an undirected graph.
See Sequence motif and Markov random field
MochiView
MochiView (Motif and ChIP Viewer) Homann OR and Johnson AD.
See Sequence motif and MochiView
Multiple EM for Motif Elicitation
Multiple Expectation maximizations for Motif Elicitation (MEME) is a tool for discovering motifs in a group of related DNA or protein sequences. Sequence motif and Multiple EM for Motif Elicitation are bioinformatics.
See Sequence motif and Multiple EM for Motif Elicitation
N-linked glycosylation
N-linked glycosylation is the attachment of an oligosaccharide, a carbohydrate consisting of several sugar molecules, sometimes also referred to as glycan, to a nitrogen atom (the amide nitrogen of an asparagine (Asn) residue of a protein), in a process called N-glycosylation, studied in biochemistry.
See Sequence motif and N-linked glycosylation
Non-coding DNA
Non-coding DNA (ncDNA) sequences are components of an organism's DNA that do not encode protein sequences.
See Sequence motif and Non-coding DNA
Nucleic acid
Nucleic acids are large biomolecules that are crucial in all cells and viruses.
See Sequence motif and Nucleic acid
Nucleic acid sequence
A nucleic acid sequence is a succession of bases within the nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule.
See Sequence motif and Nucleic acid sequence
Nucleotide
Nucleotides are organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate.
See Sequence motif and Nucleotide
Operon
In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter.
Particle swarm optimization
In computational science, particle swarm optimization (PSO) is a computational method that optimizes a problem by iteratively trying to improve a candidate solution with regard to a given measure of quality.
See Sequence motif and Particle swarm optimization
Pattern
A pattern is a regularity in the world, in human-made design, or in abstract ideas.
See Sequence motif and Pattern
Pfam
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. Sequence motif and Pfam are bioinformatics.
Phosphorylation
In biochemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion.
See Sequence motif and Phosphorylation
Phylogenetics
In biology, phylogenetics is the study of the evolutionary history and relationships among or within groups of organisms. Sequence motif and phylogenetics are bioinformatics.
See Sequence motif and Phylogenetics
Planted motif search
In the field of computational biology, a planted motif search (PMS) also known as a (l, d)-motif search (LDMS) is a method for identifying conserved motifs within a set of nucleic acid or peptide sequences. Sequence motif and planted motif search are bioinformatics.
See Sequence motif and Planted motif search
Polymer backbone
In polymer science, the polymer chain or simply backbone of a polymer is the main chain of a polymer.
See Sequence motif and Polymer backbone
Position weight matrix
A position weight matrix (PWM), also known as a position-specific weight matrix (PSWM) or position-specific scoring matrix (PSSM), is a commonly used representation of motifs (patterns) in biological sequences. Sequence motif and position weight matrix are bioinformatics.
See Sequence motif and Position weight matrix
PROSITE
PROSITE is a protein database.
See Sequence motif and PROSITE
Protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues.
See Sequence motif and Protein
Protein domain
In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest.
See Sequence motif and Protein domain
Protein I-sites
I-sites are short sequence-structure motifs that are mined from the Protein Data Bank (PDB) that correlate strongly with three-dimensional structural elements.
See Sequence motif and Protein I-sites
Protein primary structure
Protein primary structure is the linear sequence of amino acids in a peptide or protein.
See Sequence motif and Protein primary structure
Protein secondary structure
Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains.
See Sequence motif and Protein secondary structure
Protein tertiary structure
Protein tertiary structure is the three-dimensional shape of a protein.
See Sequence motif and Protein tertiary structure
Regular expression
A regular expression (shortened as regex or regexp), sometimes referred to as rational expression, is a sequence of characters that specifies a match pattern in text.
See Sequence motif and Regular expression
Regulatory sequence
A regulatory sequence is a segment of a nucleic acid molecule which is capable of increasing or decreasing the expression of specific genes within an organism.
See Sequence motif and Regulatory sequence
RNA splicing
RNA splicing is a process in molecular biology where a newly-made precursor messenger RNA (pre-mRNA) transcript is transformed into a mature messenger RNA (mRNA).
See Sequence motif and RNA splicing
Satellite DNA
Satellite DNA consists of very large arrays of tandemly repeating, non-coding DNA.
See Sequence motif and Satellite DNA
Sequence (biology)
A sequence in biology is the one-dimensional ordering of monomers, covalently linked within a biopolymer; it is also referred to as the primary structure of a biological macromolecule.
See Sequence motif and Sequence (biology)
Sequence analysis
In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. Sequence motif and sequence analysis are bioinformatics.
See Sequence motif and Sequence analysis
Sequence logo
In bioinformatics, a sequence logo is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences). Sequence motif and sequence logo are bioinformatics.
See Sequence motif and Sequence logo
Sequential pattern mining
Sequential pattern mining is a topic of data mining concerned with finding statistically relevant patterns between data examples where the values are delivered in a sequence. Sequence motif and Sequential pattern mining are bioinformatics.
See Sequence motif and Sequential pattern mining
Short linear motif
In molecular biology short linear motifs (SLiMs), linear motifs or minimotifs are short stretches of protein sequence that mediate protein–protein interaction.
See Sequence motif and Short linear motif
Signal peptide
A signal peptide (sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short peptide (usually 16-30 amino acids long) present at the N-terminus (or occasionally nonclassically at the C-terminus or internally) of most newly synthesized proteins that are destined toward the secretory pathway.
See Sequence motif and Signal peptide
Structural motif
In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a common three-dimensional structure that appears in a variety of different, evolutionarily unrelated molecules.
See Sequence motif and Structural motif
TRANSFAC
TRANSFAC (TRANScription FACtor database) is a manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles.
See Sequence motif and TRANSFAC
Translation (biology)
In biology, translation is the process in living cells in which proteins are produced using RNA molecules as templates.
See Sequence motif and Translation (biology)
Zinc finger
A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) which stabilizes the fold.
See Sequence motif and Zinc finger
References
[1] https://en.wikipedia.org/wiki/Sequence_motif
Also known as DNA motif, Sequence motifs.
, Protein primary structure, Protein secondary structure, Protein tertiary structure, Regular expression, Regulatory sequence, RNA splicing, Satellite DNA, Sequence (biology), Sequence analysis, Sequence logo, Sequential pattern mining, Short linear motif, Signal peptide, Structural motif, TRANSFAC, Translation (biology), Zinc finger.