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the original mRNA. Some clustering algorithms use single-linkage clustering, constructing a transitive closure of sequences with a similarity over a
Sequence_clustering
Grouping a set of objects by similarity
statistical distributions. Clustering can therefore be formulated as a multi-objective optimization problem. The appropriate clustering algorithm and parameter
Cluster_analysis
Agglomerative hierarchical clustering method
Complete-linkage clustering is one of several methods of agglomerative hierarchical clustering. At the beginning of the process, each element is in a cluster of its
Complete-linkage_clustering
Classification by similarity of DNA
Hierarchical clustering algorithms (HCA): uclust & cd-hit & ESPRIT Bayesian clustering: CROP In addition to similarity-based grouping, marker gene sequences can
Operational_taxonomic_unit
Clustering methods
{\displaystyle j} . The general approach to spectral clustering is to use a standard clustering method (there are many such methods, k-means is discussed
Spectral_clustering
Topics referred to by the same term
computation Nanorod, in nanotechnology and materials science Non-redundant sequence clustering, in genetics and bioinformatics NR Vulpeculae, a red supergiant star
NR
Agglomerative hierarchical clustering method
single-linkage clustering is one of several methods of hierarchical clustering. It is based on grouping clusters in bottom-up fashion (agglomerative clustering), at
Single-linkage_clustering
Vector quantization algorithm minimizing the sum of squared deviations
k-means clustering is a method of vector quantization, originally from signal processing, that aims to partition n observations into k clusters in which
K-means_clustering
Statistical method in data analysis
clusters. Strategies for hierarchical clustering generally fall into two categories: Agglomerative: Agglomerative clustering, often referred to as a "bottom-up"
Hierarchical_clustering
Bioinformatician and associate professor at Seoul National University
MMseqs2, a software suite for protein sequence searching and clustering, and Linclust, which clusters protein sequence datasets in linear time. These tools
Martin_Steinegger_(scientist)
Generalization of a sequence of points
specifically in general topology and related branches, a net or Moore–Smith sequence is a function whose domain is a directed set. The codomain of this function
Net_(mathematics)
Analysis of sets of categorical sequences
motivation behind social sequence analysts' use of optimal matching, clustering, and related methods to identify common "classes" of sequences at all levels of
Sequence analysis in social sciences
Sequence_analysis_in_social_sciences
Group of consonants without a vowel in between
§ Brackets and transcription delimiters. In linguistics, a consonant cluster, consonant sequence or consonant compound is a group of consonants which have no
Consonant_cluster
In computer science, data stream clustering is defined as the clustering of data that arrive continuously such as telephone records, multimedia data,
Data_stream_clustering
Single DNA sequences obtained from a high-throughput analysis of marker genes
operational clustering units altogether. Therefore, ASVs represent a finer distinction between sequences. ASVs are also referred to as exact sequence variants
Amplicon_sequence_variant
Continuous band of stars that appears on plots of stellar color versus brightness
In astronomy, the main sequence is a classification of stars which appear on plots of stellar color versus brightness as a continuous and distinctive band
Main_sequence
Spherical collection of stars
in the cluster with comparable luminosity and thus differs from the main-sequence stars formed early in the cluster's existence. Some clusters have two
Globular_cluster
Cluster point in a topological space
definition of a cluster or accumulation point of a sequence generalizes to nets and filters. The similarly named notion of a limit point of a sequence (respectively
Accumulation_point
a degree of belonging to clusters FLAME clustering (Fuzzy clustering by Local Approximation of MEmberships): define clusters in the dense parts of a dataset
List_of_algorithms
Database of protein sequences and functional information
50% sequence identity, respectively, to the longest sequence. Clustering sequences significantly reduces database size, enabling faster sequence searches
UniProt
Main sequence star that is more luminous and bluer than expected
identified in a stellar cluster, they have a higher effective temperature than the main sequence turnoff point for the cluster, where ordinary stars begin
Blue_straggler
Group of evolutionarily-related proteins
example: BLAST - DNA sequence similarity search BLASTp - Protein sequence similarity search OrthoFinder - Method for clustering proteins into families
Protein_family
Family of database software by Microsoft
various algorithms—Decision trees, clustering algorithm, Naive Bayes algorithm, time series analysis, sequence clustering algorithm, linear and logistic regression
Microsoft_SQL_Server
Family of DNA sequences found in prokaryotic organisms
CRISPR (/ˈkrɪspər/; acronym for clustered regularly interspaced short palindromic repeats) is a family of DNA sequences found in the genomes of prokaryotic
CRISPR
Group of stars
embedded clusters may be home to various types of young stellar objects including protostars and pre-main-sequence stars. An example of an embedded cluster is
Star_cluster
Nucleotide or amino-acid sequence pattern
sequences using clustering. Cleaning then ensures the removal of any confounding elements. Next there is the discovery stage. In this phase sequences
Sequence_motif
Brown clustering is a hard hierarchical agglomerative clustering problem based on distributional information proposed by Peter Brown, William A. Brown
Brown_clustering
Data mining technique
analysis in social sciences – Analysis of sets of categorical sequences Sequence clustering Sequence labeling Mabroukeh, N. R.; Ezeife, C. I. (2010). "A taxonomy
Sequential_pattern_mining
Metric of clustering solutions quality
Density-Based Clustering Validation (DBCV) is a metric designed to assess the quality of clustering solutions, particularly for density-based clustering algorithms
Density-based clustering validation
Density-based_clustering_validation
Type of star cluster
plotted for an open cluster, most stars lie on the main sequence. The most massive stars have begun to evolve away from the main sequence and are becoming
Open_cluster
Overview of and topical guide to machine learning
Hierarchical clustering Single-linkage clustering Conceptual clustering Cluster analysis BIRCH DBSCAN Expectation–maximization (EM) Fuzzy clustering Hierarchical
Outline_of_machine_learning
Point in stellar evolution
main sequence after its main fuel is exhausted – the main sequence turnoff. By plotting the turnoff points of individual stars in a star cluster one can
Main_sequence_turnoff
Diagram with a treelike structure
clustering, it illustrates the arrangement of the clusters produced by the corresponding analyses. in computational biology, it shows the clustering of
Dendrogram
Model-based clustering in statistics
basis for clustering, and ways to choose the number of clusters, to choose the best clustering model, to assess the uncertainty of the clustering, and to
Model-based_clustering
Algorithm in genetics published in 2010
simple clustering criteria, in regard to the requested similarity threshold T. The first criterion states that any given cluster's centroid sequence will
UCLUST
Real-valued function that quantifies similarity between two objects
Euclidean distance, which is used in many clustering techniques including K-means clustering and Hierarchical clustering. The Euclidean distance is a measure
Similarity_measure
Dim, low mass stars on the main sequence
massive, smallest, least luminous, and coolest kind of star on the main sequence. Red dwarfs are by far the most common type of fusing star in the Milky
Red_dwarf
Sequence of data points over time
series data may be clustered, however special care has to be taken when considering subsequence clustering. Time series clustering may be split into whole
Time_series
Square matrix containing the distances between elements in a set
closer in the phylogenetic tree. Hence, it builds the tree by clustering similar sequences iteratively. The method works by building the phylogenetic tree
Distance_matrix
Epidemiology method
methods of genetic clustering have been described in the literature. Genetic clustering provides a way of dealing with sequences from rapidly evolving
Source_attribution
reduces significantly the time of estimation of the similarity of sequences. Clustering data is a tool used to simplify statistical analysis of a genomic
Computational_genomics
Target peptide sequence
receptor clustering and dynamic reorganization because of its potential understanding to use for designing targeted therapeutics. The similar sequence HDEL
KDEL_(amino_acid_sequence)
published studies. Bioinformatics Homology (biology) Sequence homology Protein family Sequence clustering Emms, David M; Kelly Steven (2015). "OrthoFinder:
OrthoFinder
Physical theory of the cosmos
gravitational clustering, and is found to have only about 30% of the critical density. Since theory suggests that dark energy does not cluster in the usual
Big_Bang
Galaxy morphological classification scheme advocated by Edwin Hubble
The Hubble sequence is a morphological classification scheme for galaxies published by Edwin Hubble in 1926. It is often colloquially known as the Hubble
Hubble_sequence
Scatter plot of stars showing the relationship of luminosity to stellar classification
taken by pre-main-sequence stars in the Hertzsprung–Russell diagram Hess diagram – Diagram of stars in astronomy Red clump – Clustering of stars in astronomy
Hertzsprung–Russell_diagram
Class of commutative rings
B2 and G2. However if |b12b21| ≥ 4 then the sequence of cluster variables is not periodic and the cluster algebra is of infinite type. Suppose we start
Cluster_algebra
binary tree, it defines a hierarchical clustering of its leaves: for each edge (u,v) in T there is a cluster consisting of the leaves that are closer
Unrooted_binary_tree
KHOPCA is an adaptive clustering algorithm originally developed for dynamic networks. KHOPCA ( k {\textstyle k} -hop clustering algorithm) provides a
KHOPCA_clustering_algorithm
Sequence of points far from previous points
same sequence of points was popularized by Gonzalez (1985), who used it as part of greedy approximation algorithms for two problems in clustering, in which
Farthest-first_traversal
Data processing algorithm
Automatic clustering algorithms are algorithms that can perform clustering without prior knowledge of data sets. In contrast with other clustering techniques
Automatic clustering algorithms
Automatic_clustering_algorithms
Star cluster in the constellation of Taurus
Astronomers estimate that the cluster will survive for approximately another 250 million years, after which the clustering will be lost due to gravitational
Pleiades
Molecular structures and ubiquitous inorganic cofactors found in all domains of life
of ambidoxins: de novo maquettes that consist of 12 residues with the sequence X-Cys-X2-Cys-X2-Cys-X2-Cys-X (X = Arg, Lys), which can successfully perform
Iron–sulfur_cluster
Culture Collection
Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering". Applied and Environmental
International Collection of (Vesicular) Arbuscular Mycorrhizal Fungi
International_Collection_of_(Vesicular)_Arbuscular_Mycorrhizal_Fungi
Shared ancestry between DNA, RNA or protein sequences
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of
Sequence_homology
Group of languages of the 5th century BCE – 12th century CE
/ʋɦ/, ñh /ɲɦ/, ṇh /ɳɦ/, nh /n̪ɦ/, and mh /mɦ/ are all treated as a sequence/cluster of two consonants. Word-medially, they are permitted. Word-initially
Prakrit
Agglomerative hierarchical clustering method
algorithm. Neighbor-joining Cluster analysis Single-linkage clustering Complete-linkage clustering Hierarchical clustering Models of DNA evolution Molecular
UPGMA
Multiple star system in the constellation Carina
There are several dozen early O class stars (O3 and O4) in the cluster, mostly main sequence stars. There are just a handful of giants and supergiants including:
HD_97950
Molecule produced by a living organism
different sequence) cluster to form a protein, quaternary structure of protein is formed. Quaternary structure is an attribute of polymeric (same-sequence chains)
Biomolecule
Type of sport similar to figure skating
Pattern Sequence corresponding to the required steps from a compulsory dance and three of: Travelling Sequence, Cluster Sequence, Footwork Sequence and Artistic
Artistic_roller_skating
used an algorithm based on progressive alignment, in which the sequences were clustered with the help of the fast Fourier transform. Subsequent versions
MAFFT
Family of random graph models
above, the global clustering coefficient is an inverse function of the network size, so for large configuration networks, clustering tends to be small
Configuration_model
Submerged caldera in the Aegean Sea
event rate, magnitude–frequency behavior (b-value), and spatiotemporal clustering. They identify four stages: (1) An initial volcano-driven phase beginning
Santorini_caldera
Methods in computational biology
Alignment-free approaches have been used in sequence similarity searches, clustering and classification of sequences, and more recently in phylogenetics (Figure
Alignment-free sequence analysis
Alignment-free_sequence_analysis
Group of genes
for a more reasonable classification of the central group. From clustering sequences and plotting their occurrence onto a phylogenetic tree of the animal
Hox_gene
List of people involved in the production of media
a separate sequence of their own, the correct term is a title sequence (e.g., the familiar James Bond and The Pink Panther title sequences). Opening credits
Credits
Open cluster in the constellation Cancer
origins. Both clusters also contain red giants and white dwarfs, which represent later stages of stellar evolution, along with many main sequence stars. The
Beehive_Cluster
All genetic material of an organism
been sequenced and various regions have been annotated. The first genome to be sequenced was that of the virus φX174 in 1977; the first genome sequence of
Genome
Group of related genes in genomic DNA
gene clusters can vary significantly, from a few genes to several hundred genes. Portions of the DNA sequence of each gene within a gene cluster are found
Gene_cluster
DNA sequencing method
process of sequence by synthesis repeats for the reverse strand. The sequencing occurs for millions of clusters at once, and each cluster has ~1,000 identical
Illumina_dye_sequencing
Stellar classification
A G-type main-sequence star is a main-sequence star of spectral type G. The spectral luminosity class is V. Such a star has about 0.9 to 1.1 solar masses
G-type_main-sequence_star
Five-star system in the constellation Orion
peculiar A1 main sequence star HD 37564, an A8 young stellar object V1147 Ori, a B9.5 giant and α2 CVn variable HD 37686, a B9.5 main sequence star close to
Sigma_Orionis
Open cluster in the constrellation Hydrus
pre–main sequence stars are still enshrouded in dust but are visible to the Spitzer Space Telescope at infrared wavelengths. The cluster is of particular
NGC_602
a sequence that characterize the sequence. In Sequence analysis in social sciences, representative sequences are used to summarize sets of sequences describing
Representative_sequences
Six stacked horizontal lines used in Chinese divination
Hexagram (is found by changing all the lines into their opposite) Hexagram of Sequence Nuclear (Mutual) Hexagram (hù guà) (is found by taking the inner lines
Hexagram_(I_Ching)
Item sequences in computational linguistics
An n-gram is a sequence of n adjacent symbols in a particular order. The symbols may be n adjacent letters (including punctuation marks and blanks), syllables
N-gram
Model of communication
Poole theorized that decision making occurs in clusters of linking communication. The multiple sequence model defines different contingency variables such
Poole's multiple sequence model
Poole's_multiple_sequence_model
Galaxy cluster in the constellation of Leo
Leo Cluster. The first consists of elliptical galaxies that seem to be roughly as old as the universe. The second subpopulation contains red-sequence lenticular
Leo_Cluster
and Clustering. Springer. p. 112. ISBN 0-7923-4159-7. Retrieved 10 February 2014. von Luxburg, Ulrike (2007). "A Tutorial on Spectral Clustering" (PDF)
Indicator_vector
Compilation of software used to produce phylogenetic trees
"MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences". Bioinformatics. 37 (21): 3947–3949. doi:10.1093/bioinformatics/btab430
List of phylogenetics software
List_of_phylogenetics_software
Protein-coding gene in the species Homo sapiens
cDNAs from human T cells map to nine different chromosomes with apparent clustering". American Journal of Human Genetics. 48 (4): 726–40. PMC 1682948. PMID 2014798
ZNF37A
traditional clusters. MG-RAST has been developed in an effort to have a free, public resource for the analysis and the storage of metagenome sequence data.
MG-RAST
Type of data structure
for sequence CRDTs. MUTE is an online web-based peer-to-peer real-time collaborative editor relying on the LogootSplit algorithm. Industrial sequence CRDTs
Conflict-free replicated data type
Conflict-free_replicated_data_type
American computational biologist
approach exploits the fact that genomic sequences cluster in dense groups of near-identical sequences, allowing each cluster to be summarized by a representative
Bonnie_Berger
Japanese molecular biologist (born 1959)
is a Japanese molecular biologist, known for discovering the DNA sequence of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR). Ishino
Yoshizumi_Ishino
these BGCs into gene cluster families (GCFs). BiG-SLiCE (Biosynthetic Genes Super-Linear Clustering Engine), a tool designed to cluster massive numbers of
Metabolic_gene_cluster
Large self-illuminated object in space
Giuseppe (2020). "Clustering of Local Group Distances: Publication Bias or Correlated Measurements? VI. Extending to Virgo Cluster Distances". The Astrophysical
Star
Algorithm that generates an approximation of a random number sequence
generating a sequence of numbers whose properties approximate the properties of sequences of random numbers. The PRNG-generated sequence is not truly
Pseudorandom_number_generator
Densest star cluster known
and more massive than O5 have evolved away from the main sequence, while the Quintuplet Cluster includes a number of hot supergiants as well as a red supergiant
Arches_Cluster
Star in the constellation Fornax
Vbn, indicating that it is instead a slightly less luminous A-type main-sequence star with broad or nebulous absorption lines due to rapid rotation. It
Chi1_Fornacis
Process of determining the nucleic acid sequence
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is
DNA_sequencing
Data structure for query optimization in databases
and ORDER BY clauses. There can be more than one non-clustered index on a database table. Clustering alters the data block into a certain distinct order
Database_index
Dense musical chord
associated with the sound mass aesthetic, containing, "one of the largest clustering of individual pitches that has been written", Krzysztof Penderecki's Threnody
Tone_cluster
Type of star larger than main-sequence but smaller than a giant
O B A F G K M L T Brown dwarfs White dwarfs Red dwarfs Subdwarfs Main sequence ("dwarfs") Subgiants Giants Red giants Blue giants Bright giants Supergiants
Subgiant
Classification of stars based on spectral properties
and 9 being coolest (e.g., A8, A9, F0, and F1 form a sequence from hotter to cooler). The sequence has been expanded with three classes for other stars
Stellar_classification
In mathematics, a Somos sequence is a sequence of numbers defined by a certain recurrence relation, described below. They were discovered by mathematician
Somos_sequence
Pattern of similarities in human populations
ancestry, with divisions between clusters aligning largely with geographic barriers such as oceans or mountain ranges. Clustering studies have been applied to
Human_genetic_clustering
Bottom-up clustering method for creating phylogenetic trees
In bioinformatics, neighbor joining is a bottom-up (agglomerative) clustering method for the creation of phylogenetic trees, created by Naruya Saitou and
Neighbor_joining
Continuous progression from past to future
causality, being a component quantity of various measurements used to sequence events, to compare the duration of events (or the intervals between them)
Time
Computational analysis of large, complex sets of biological data
Examples of clustering algorithms applied in gene clustering are k-means clustering, self-organizing maps (SOMs), hierarchical clustering, and consensus
Bioinformatics
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