Python Programming for Biology: Bioinformatics and Beyond

(bioinformatics):

Spectrum (signal

processing):

Spin active (chemistry):

Splice (molecular

biology):

Stack (computing):

Standard deviation

(mathematics):

Standard normal

distribution

(mathematics):

Statement (computing):

Stem-loops (molecular

biology):

Also called a Sobel filter. A matrix which is convolved with a

pixmap image for the purpose of detecting contrast changes (i.e.

edges) along a horizontal or vertical direction. Effectively this

creates a secondary image where the signal gives an

approximation of the gradient of intensity changes in the

primary image.

Bits of geometric information that relate to the spatial

conformation of an object, such as a protein structure, which

when considered in combination help determine the overall

three-dimensional shape.

An experimental signal viewed in terms of frequency, rather

than time or space.

With reference to atoms, a nucleus which exhibits nuclear

magnetic resonance, i.e. absorbs characteristic radio frequencies

when placed in a magnetic field.

To join together two biopolymer chains. Splicing notably occurs

in the processing of messenger rRNA modules, where the

unwanted parts, introns, are removed and the remainder (which

generally contains the protein-coding region) are joined

together.

A collection of items that are processed in the order ‘first in, last

out’.

A measure of the spread of values from their mean. Calculated

as the square root of the average square difference between the

values and the mean.

A normal distribution with mean 0 and standard deviation 1.

The smallest logical elements of a computer program.

Small regions of double-stranded nucleic acid, usually RNA,

where a single chain folds back and base-pairs with itself.

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Strand (molecular

biology):

String (computing):

Structural environment

(bioinformatics):

Structure ensemble

(bioinformatics):

Student’s T distribution

(mathematics):

Subclass (computing):

Substitutable (molecular

biology):

Substitution (molecular

biology):

Substitution matrix

(bioinformatics):

One nucleic acid chain molecule. DNA usually has two nucleic

acid strands joined along their length by hydrogen-bonded base

pairs; the strands go in the opposite directions, in terms of the

chemical bonds.

A computational data type representing an ordered collection of

characters that form a piece of text.

The categories of local three-dimensional conformation within a

biological molecule. Generally with reference to the different

features found in protein structure that affect the nature of

residue substitution during evolution. Environment categories

typically correspond to secondary structure, hydrogen bonding

and solvent accessibility states.

A representation of a molecule’s three-dimensional structure,

consisting of a collection of alternative models (i.e. sets of

coordinates) which together represent the variability or

uncertainty in the data. Often the models of an ensemble

represent alternative conformations which all fit with the

experimental data.

Used in various statistical tests including determining

confidence intervals on the mean of a distribution given a

sampling, i.e. whether two means are significantly different.

With reference to object-oriented programming, a subclass is a

type of object definition that is based on, i.e. inherits from,

another type of object, called the superclass.

The ability of two different types of residue to swap with one

another (in a DNA or protein chain) during evolution.

The swapping during evolution of one residue type for another

in a given position of a biological polymer molecule.

Also called a similarity matrix. A means of representing the

equivalence between different types of residue in a sequence

alignment. Described in the form of a table, so that a score may

be obtained for each possible pair of residue type. This provides

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Superclass (computing):

Supervised learning