Python Programming for Biology: Bioinformatics and Beyond

(molecular biology):

Palette (graphics):

Parallel tempering

(computing):

Paralogues (molecular

biology):

Parent-child relationship

(computing):

Parsimony

(bioinformatics):

Path (computing):

Pearson’s chi-squared

test (mathematics):

Pearson’s correlation

coefficient

A pair of experimentally determined DNA sequences (reads)

which are known to come from either end of the same fragment

of DNA.

A limited array of colours used as a look-up table to construct

an image. Using a colour palette gives smaller images because

colours are referred to by index, rather than by value, but the

range of colour available for the image is limited.

Also called replica exchange, is a variant of the Markov chain

Monte Carlo method that uses parallel implementations at

different ‘temperatures’, i.e. where higher temperatures allow

greater variation between subsequent steps. The temperatures of

parallel computations are swapped so that each can explore a

large number of states in an unbiased manner.

Entities which are homologous, sharing a common ancestor,

because of a gene duplication event. Effectively finding closely

related genes or proteins inside one organism.

When referring to data models, the relationship between objects

stating that one is formally contained by the other; the parent

contains the child. For example a molecule object may contain

atom objects. This containment hierarchy usually involves

objects of completely different types and is distinct from the

super- to subclass relationship.

The principle of the most likely evolutionary route, which for

example has generated divergent sequences, being the one that

involves the fewest changes, i.e. the most frugal.

The location of a file stored in a file system, e.g. on disk,

described as a path through a hierarchical directory structure.

In statistics, a test, first discussed by Karl Pearson, for a null

hypothesis that a distribution determined from a measured

sample is consistent with the distribution provided by a model.

In statistics, a measure of the linear correlation between two

distributions, usually provided by paired measurements of a

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(mathematics):

Percent point function

(mathematics):

Perl (computing):

pH (chemistry):

Phase (signal

processing):

Phasing (signal

processing):

Phylogenetic tree

(bioinformatics):

pI (chemistry):

Pickle (computing):

Pixel (graphics):

Pixmap (computing):

sample.

A function that determines the confidence interval around the

sample mean, given a specified confidence level.

A programming language, which like Python is high level and

interpreted. Perl is an older language than Python, and is

popular in the bioinformatics community.

The negative logarithm of the hydrogen ion concentration of a

solution; a measure of the acidity where a value of 7.0 is

neutral; lower than this is acidic and greater than this is alkaline.

In certain applications, this describes the amount by which the

real and imaginary parts of a complex signal need to be rotated

in order to put them into a form that provides a purer description

of the signal, which can help in interpretation of the signal.

The process whereby a complex signal has its phase corrected in

some situations.

A hierarchical data structure used to describe the evolutionary

relationship between biological entities, such as whole

organisms or single macromolecules.

The isoelectric point; the pH at which a molecule has no overall

charge, where positive and negative charged chemical groups

balance. The pI is a property of a molecule that depends on the

number and relative strengths of its acidic and basic groups.

The Python method of serialising data, automatically converting

in-memory data structures into a stream of data that may be

stored on disk, typically a plain text file.

The smallest square area of colour with which a computer

image is constructed.

A rectangular array of colour intensity values that describe the

pixels of an image.

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