UCLUST
is an
algorithm
In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific Computational problem, problems or to perform a computation. Algorithms are used as specificat ...
designed to cluster
nucleotide
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...
or
amino-acid sequences into clusters based on sequence similarity. The algorithm was published in 2010 and implemented in a program also named UCLUST. The algorithm is described by the author as following two simple clustering criteria, in regard to the requested similarity threshold T. The first criterion states that any given cluster's centroid sequence will have a similarity smaller than T to any other clusters' centroid sequence. The second criterion states that each member sequence in a given cluster will have similarity to the cluster's centroid sequence that is equal or greater than T.
UCLUST algorithm is a greedy one. As a result, the order of the sequences in the input file will affect the resulting clusters and their quality. For this reason, it is advised that the sequences will be sorted before entering clustering stage. The program UCLUST is equipped with some options to sort the input sequences prior to clustering them.
UCLUST program is widely utilized among the
bioinformatic
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combine ...
research community, where it used for multiple applications including OTU assignment (e.g. 16s), creating non-redundant
gene
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
catalogs,
taxonomic
Taxonomy is the practice and science of categorization or classification.
A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. ...
assignment and
phylogenetic analysis.
External links
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See also
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Sequence clustering In bioinformatics, sequence clustering algorithms attempt to group biological sequences that are somehow related. The sequences can be either of genomic, "transcriptomic" ( ESTs) or protein origin.
For proteins, homologous sequences are typicall ...
References
{{Reflist
2010 software
Bioinformatics algorithms
Metagenomics