Python Programming for Biology: Bioinformatics and Beyond

(mathematics):

Coding strand

(molecular biology):

Codon (molecular

biology):

Collection (computing):

Colour space (graphics):

Comparative modelling

(bioinformatics):

Compilation

(computing):

The part of a computer application that interacts with the user,

typically as a result of using a service on a remote server.

For a collection of data items, the process of grouping similar

items together into a number of clusters. The number of groups

may or may not be known ahead of time but a data item is

allocated to only one cluster. Clustering works by changing the

membership of data items in cluster groups to maximise

similarity of items within clusters and minimise the similarity of

items between clusters.

In a double-stranded DNA chain that contains a gene, the coding

strand is the one that is reproduced as RNA, in terms of

sequence, when the DNA is read.

A group of three nucleotide residues that specify the

incorporation of a particular kind of amino acid into a given

position of a protein chain.

The grouping of otherwise separate data items into a container

data structure, which may be referred to as a distinct entity. In

Python the usual collection types are lists, sets, tuples and

dictionaries.

The notion of describing colours as vector locations, relative to

colour axes, which describe the component properties (e.g. red,

green and blue) of colours.

The process by which the three-dimensional structures of

proteins may be predicted by comparison to similar proteins

with experimentally determined structures. If two proteins are

inferred to be homologous (evolutionarily related) by virtue of

sequence similarity, then because structure is more conserved

than sequence the known structure of one protein can be used as

a template to determine the fold of the other.

The process of converting textual source code, which is

generally independent of any particular kind of computer, into

executable binary code that may be run on computers with a

specific type of processor architecture.

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Complement

(mathematics):

Complementarity

(molecular biology):

Complex (molecular

biology):

Composition

(mathematics):

Conditional probability

(mathematics):

Conditional statement

(computing):

Confidence level

(mathematics):

Conformation

(chemistry):

Consensus sequence

(bioinformatics):

Conservation (molecular

In set theory, the elements that are not in a specified set.

The relationship between two molecules where the chemical

properties of one complement those of the other, and so allow a

tight interaction. This is often used to describe aromatic base

pairs between nucleotides, which form hydrogen bonds across a

DNA duplex. Accordingly A and T residues are complementary

and likewise C and G.

Two or more biological molecules that bind to one another in a

specific manner to form a larger particle.

The application of two transformations, e.g. by matrix

multiplications, one after the other.

The probability that one event occurs given the condition that

some other event has occurred.

A means of controlling the flow of a program’s execution, doing

different things depending on whether some test turns out to

give true or false. In Python this is done with if, elif and else

statements.

In statistics, the probability that a measurement will be within

some specified range of values.

For a molecule, one specific three-dimensional shape from

amongst a range of many possible shapes. Different

conformations may be similar to one another, e.g. if a protein

has a compact fold, and a set of conformations can represent the

dynamics or uncertainty of a structure.

A consensus sequence represents the average of all the

sequences in a sequence alignment, and thus not usually a real

biological sequence. Each position in the consensus may reflect

the most common residue observed at that position or the

average residue properties of that position.

The tendency of a biological feature, such as a sequence or a 3D

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