Python Programming for Biology: Bioinformatics and Beyond

(chemistry):

Dihedral angle

(mathematics):

Dimension

(mathematics):

Dimensional reduction

(mathematics):

Discrete (mathematics):

Discrete Fourier

transform (computing):

When considering the smallest component process of a dynamic

system, detailed balance is reached when the system is at

equilibrium and the reverse of each micro-process restores

equilibrium. In Markov chains, when using the Metropolis-

Hastings criterion, detailed balance is used to test whether the

chain has reached the required equilibrium state.

A collection data type in Python (equivalent to a Perl hash and a

Java hash map) where data items are held in pairs such that a

unique key is used to look up a corresponding value from the

dictionary.

The primary experimental data collected in X-ray

crystallography, which may be used to determine the three-

dimensional structures of molecules. The diffraction pattern is

created when a beam of X-ray radiation irradiates a regular

crystal lattice, effectively reflecting from the different atomic

planes in the crystal.

Also called torsion angle, is a measure of twist between two

planes. A dihedral angle can be measured for an ordered list of

four points; the first three points define one plane and the last

three the second plane, such that the angle of twist is around the

central two points which the planes share.

The number of independent axes (or features) that describe a

location within a given parameter space. A dimension may also

refer to one of those independent axes, e.g. the ‘depth’

dimension.

The practice of representing a set of data using fewer

dimensions than the original data, for example by using

projection. Often the aim of dimensional reduction is to render

the data more amenable to analysis while still preserving the

essential features of the data.

Where a quantity is represented in terms of the whole numbers,

rather than as a continuum of real values.

The Fourier transform (converting a signal from time to

frequency) applied to a data series with discrete, rather than

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Discrete-time

homogeneous Markov

chain (computing):

Discrimination

(computing):

Disjoint (mathematics):

Distance matrix

(mathematics):

Distribution

(mathematics):

Disulphide (chemistry):

DNA (biology):

DNA sequence (

molecular biology):

continuous, time points.

A Markov chain with discrete, rather than continuous, positions

in the chains (time), and where the transition probabilities

between states do not depend on chain position (or time).

The process of allocating data points into distinct categories or

clusters. In computing this may be a predictive method rather

than an unambiguous classification.

In probability, two events that do not intersect, and so share no

common outcome.

A rectangular array of values representing the distances between

items, where each item corresponds to a different row and/or

column in the matrix. The distance may be a conventional

geometric distance or some other metric that measures the

similarity or separation between data items.

An assignment of a probability to each possible, measureable

outcome.

A chemical group consisting of two covalently linked sulphur

atoms. Disulphide groups are often present in proteins found

outside cells (an oxidising environment), linking the side chains

of two cysteine residues.

2′-Deoxyribonucleic acid, the long-chain molecule that is the

main store of genetic information; the template for making RNA

and proteins and the means by which genes are inherited.

The sequential order of the four different types of nucleotide

compound that make up a linear DNA chain. Although DNA is

a double strand, containing two tightly bound chains, because

the residues of the chains are complementary the sequence of

one strand is automatically known from the other. When

referring to genes it is conventional to refer to the DNA

sequence of the coding strand.

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Domains (molecular