Bioinformatics Glossary


Machine learning(机器学习)
The training of a computational model of a process or classification scheme to distinguish between alternative possibilities.

Markov chain(马尔可夫链)
Describes a process that can be in one of a number of states at any given time. The Markov chain is defined by probabilities for each transition occurring; that is, probabilities of the occurrence of state sj given that the current state is sp Substitutions in nucleic acid and protein sequences are generally assumed to follow a Markov chain in that each site changes independently of the previous history of the site. With this model, the number and types of substitutions observed over a relatively short period of evolutionary time can be extrapolated to longer periods of time. In performing sequence alignments and calculating the statistical significance of alignment scores, sequences are assumed to be Markov chains in which the choice of one sequence position is not influenced by another.

Masking (过滤)
Also known as Filtering. The removal of repeated or low complexity regions from a sequence in order to improve the sensitivity of sequence similarity searches performed with that sequence.

Maximum likelihood (phylogeny, alignment)(最大似然法)
The most likely outcome (tree or alignment), given a probabilistic model of evolutionary change in DNA sequences.

Maximum parsimony(最大简约法)
The minimum number of evolutionary steps required to generate the observed variation in a set of sequences, as found by comparison of the number of steps in all possible phylogenetic trees.

Method of moments
The mean or expected value of a variable is the first moment of the values of the variable around the mean, defined as that number from which the sum of deviations to all values is zero. The standard deviation is the second moment of the values about the mean, and so on.

Minimum spanning tree
Given a set of related objects classified by some similarity or difference score, the mini-mum spanning tree joins the most-alike objects on adjacent outer branches of a tree and then sequentially joins less-alike objects by more inward branches. The tree branch lengths are calculated by the same neighbor-joining algorithm that is used to build phylogenetic trees of sequences from a distance matrix. The sum of the resulting branch lengths between each pair of objects will be approximately that found by the classification scheme.

MMDB (分子建模数据库)
Molecular Modelling Database. A taxonomy assigned database of PDB (see PDB) files, and related information.

Molecular clock hypothesis(分子钟假设)
The hypothesis that sequences change at the same rate in the branches of an evolutionary

Monte Carlo(蒙特卡罗法)
A method that samples possible solutions to a complex problem as a way to estimate a more general solution.

Motif (模序)
A short conserved region in a protein sequence. Motifs are frequently highly conserved parts of domains.

Multiple Sequence Alignment (多序列联配)
An alignment of three or more sequences with gaps inserted in the sequences such that residues with common structural positions and/or ancestral residues are aligned in the same column. Clustal W is one of the most widely used multiple sequence alignment programs

Mutation data matrix(突变数据矩阵,即PAM矩阵)
A scoring matrix compiled from the observation of point mutations between aligned sequences. Also refers to a Dayhoff PAM matrix in which the scores are given as log odds scores.

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