Bioinformatics Glossary


CDS or cds (编码序列)
Coding sequence.

Chebyshe, d inequality
The probability that a random variable exceeds its mean is less than or equal to the square of 1 over the number of standard deviations from the mean.

Clone (克隆)
Population of identical cells or molecules (e.g. DNA), derived from a single ancestor.

Cloning Vector (克隆载体)
A molecule that carries a foreign gene into a host, and allows/facilitates the multiplication of that gene in a host. When sequencing a gene that has been cloned using a cloning vector (rather than by PCR), care should be taken not to include the cloning vector sequence when performing similarity searches. Plasmids, cosmids, phagemids, YACs and PACs are example types of cloning vectors.

Cluster analysis(聚类分析)
A method for grouping together a set of objects that are most similar from a larger group of related objects. The relationships are based on some criterion of similarity or difference. For sequences, a similarity or distance score or a statistical evaluation of those scores is used.

A single sequence that represents the most conserved regions in a multiple sequence alignment. The BLOCKS server uses the cobbler sequence to perform a database similarity search as a way to reach sequences that are more divergent than would be found using the single sequences in the alignment for searches.

Coding system (neural networks)
Regarding neural networks, a coding system needs to be designed for representing input and output. The level of success found when training the model will be partially dependent on the quality of the coding system chosen.
Codon usageAnalysis of the codons used in a particular gene or organism.

Clusters of orthologous groups in a set of groups of related sequences in microorganism and yeast (S. cerevisiae). These groups are found by whole proteome comparisons and include orthologs and paralogs. See also Orthologs and Paralogs.

Comparative genomics(比较基因组学)
A comparison of gene numbers, gene locations, and biological functions of genes in the genomes of diverse organisms, one objective being to identify groups of genes that play a unique biological role in a particular organism.

Complexity (of an algorithm)(算法的复杂性)
Describes the number of steps required by the algorithm to solve a problem as a function of the amount of data; for example, the length of sequences to be aligned.

Conditional probability(条件概率)
The probability of a particular result (or of a particular value of a variable) given one or more events or conditions (or values of other variables).

Conservation (保守)
Changes at a specific position of an amino acid or (less commonly, DNA) sequence that preserve the physico-chemical properties of the original residue.

A single sequence that represents, at each subsequent position, the variation found within corresponding columns of a multiple sequence alignment.

Context-free grammars
A recursive set of production rules for generating patterns of strings. These consist of a set of terminal characters that are used to create strings, a set of nonterminal symbols that correspond to rules and act as placeholders for patterns that can be generated using terminal characters, a set of rules for replacing nonterminal symbols with terminal characters, and a start symbol.

Contig (序列重叠群/拼接序列)
A set of clones that can be assembled into a linear order. A DNA sequence that overlaps with another contig. The full set of overlapping sequences (contigs) can be put together to obtain the sequence for a long region of DNA that cannot be sequenced in one run in a sequencing assay. Important in genetic mapping at the molecular level.

The Common Object Request Broker Architecture (CORBA) is an open industry standard for working with distributed objects, developed by the Object Management Group. CORBA allows the interconnection of objects and applications regardless of computer language, machine architecture, or geographic location of the computers.

Correlation coefficient(相关系数)
A numerical measure, falling between - 1 and 1, of the degree of the linear relationship between two variables. A positive value indicates a direct relationship, a negative value indicates an inverse relationship, and the distance of the value away from zero indicates the strength of the relationship. A value near zero indicates no relationship between the variables.

Covariation (in sequences)(共变)
Coincident change at two or more sequence positions in related sequences that may influence the secondary structures of RNA or protein molecules.

Coverage (or depth) (覆盖率/厚度)
The average number of times a nucleotide is represented by a high-quality base in a collection of random raw sequence. Operationally, a 'high-quality base' is defined as one with an accuracy of at least 99% (corresponding to a PHRED score of at least 20).

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