A space introduced into an alignment to compensate for insertions and deletions in one sequence relative to another. To prevent the accumulation of too many gaps in an alignment, introduction of a gap causes the deduction of a fixed amount (the gap score) from the alignment score. Extension of the gap to encompass additional nucleotides or amino acid is also penalized in the scoring of an alignment.

Gap penalty（空位罚分）

A numeric score used in sequence alignment programs to penalize the presence of gaps within an alignment. The value of a gap penalty affects how often gaps appear in alignments produced by the algorithm. Most alignment programs suggest gap penalties that are appropriate for particular scoring matrices.

Genetic algorithm（遗传算法）

A kind of search algorithm that was inspired by the principles of evolution. A population of initial solutions is encoded and the algorithm searches through these by applying a pre-defined fitness measurement to each solution, selecting those with the highest fitness for reproduction. New solutions can be generated during this phase by crossover and mutation operations, defined in the encoded solutions.

Genetic map （遗传图谱）

A genome map in which polymorphic loci are positioned relative to one another on the basis of the frequency with which they recombine during meiosis. The unit of distance is centimorgans (cM), denoting a 1% chance of recombination.

Genetic mutation （遗传变异）

A change in the nucleotide sequence of a DNA molecule. Genetic mutations are a kind of genetic polymorphism. The term "mutation," as opposed to "polymorphism," is generally used to refer to changes in DNA sequence which are not present in most individuals of a species and either have been associated with disease (or risk of disease) or have resulted from damage inflicted by external agents (such as viruses or radiation).

Genetic polymorphism （遗传多样性）

A difference in DNA sequence among individuals, groups, or populations (e.g. a genetic polymorphism might give rise to blue eyes versus brown eyes, or straight hair versus curly hair). Genetic polymorphisms may be the result of chance processes, or may have been induced by external agents (such as viruses or radiation). If a difference in DNA sequence among individuals has been shown to be associated with disease, it will usually be called a genetic mutation. Changes in DNA sequence which have been confirmed to be caused by external agents are also generally called "mutations" rather than "polymorphisms."

Genome（基因组）

The genetic material of an organism, contained in one haploid set of chromosomes.

Gibbs sampling method

An algorithm for finding conserved patterns within a set of related sequences. A guessed alignment of all but one sequence is made and used to generate a scoring matrix that represents the alignment. The matrix is then matched to the left-out sequence, and a probable location of the corresponding pattern is found. This prediction is then input into a new alignment and another scoring matrix is produced and tested on a new left-out sequence. The process is repeated until there is no further improvement in the matrix.

Global alignment（整体联配）

Attempts to match as many characters as possible, from end to end, in a set of twomore sequences.

Gopher （一个文档发布系统，允许检索和显示文本文件）

Graph theory（图论）

A branch of mathematics which deals with problems that involve a graph or network structure. A graph is defined by a set of nodes (or points) and a set of arcs (lines or edges) joining the nodes. In sequence and genome analysis, graph theory is used for sequence alignments and clustering alike genes.

GSS（基因综述序列）

Genome survey sequence.

GUI（图形用户界面）

Graphical user interface.

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ZHANGroup : BioinformaticsGlossaryG

Bioinformatics Glossary

G

gap （空位/间隙/缺口）