Python Programming for Biology: Bioinformatics and Beyond



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[Tim J. Stevens, Wayne Boucher] Python Programming

(mathematics):

Intron (molecular



biology):

Isoelectric point



(chemistry):

Iterable (computing):

Iterate (computing):

Iterator (computing):

Java (computing):

A specification for the functionality provided by a class or

module, without worrying about how that functionality is

actually implemented.

The common elements between two collections, usually sets.

The non-coding parts in the middle of genes. Intron sequences

are initially transcribed into RNA, but are removed to make

mature RNA molecules, and so do not contribute to the final

product. Introns separate a gene’s exons, which do form the

mature RNA and thus may encode protein sequence.

The pH at which a molecule has no overall charge; naturally

only relevant for molecules that contain acidic and/or basic

chemical groups.

A property whereby an object can provide the individual

members from a group of items, e.g. from a list. In Python an

iterable object can be used to provide a sequence of items, such

as in a ‘for’ loop. This is a concept distinct from the iterator

object (see below), though all iterable objects can be converted

into iterators using the iter() function.

The process of repeating the same basic operation a number of

times, such as extracting all the items from a list in sequence. In

the context of algorithms this might be to improve the solution

to a problem, where the solution to one cycle serves as a

foundation for the next.

An object that emits a succession of items, by continually

asking for the ‘next’ item until all items have been considered.

In Python an iterator is a special kind of object that provides the

next item in a data sequence via its __next()__ method (in

Python 3; next() in Python 2). In this context an iterator is

distinct from an iterable, which does not support the __next()__

method but which can nonetheless be used in loops etc. All

iterators are iterable but not vice versa.

A compiled, object-oriented programming language commonly

used for database and internet applications.




Join (computing):

K

a



(chemistry):

K-dimensional trees



(computing):

Kernel methods



(computing):

Kernel trick



(mathematics):

Key, value (computing):



k-nearest neighbour

(computing):

Kohonen map



(computing):

Layout (graphics):

With regard to databases the way information can be linked

across different tables.

A symbolic abbreviation for the acid dissociation constant.

A way of grouping data with K dimensions (independent data

axes) into a tree-like structure, i.e. a hierarchy of branching

nodes. Such an arrangement can make particular operations,

such as finding data points within a given radius, more efficient.

The basic notion is that the tree arrangement means that only

some of the data needs to be checked.

A type of algorithm used for machine learning (pattern

recognition) where the original data are placed in a vector space

so that the data may be analysed in terms of the distance

between points. Such methods often use a kernel function to

efficiently calculate the coincidence or similarity (inner product)

between data points.

The means by which a kernel method uses a kernel function to

effectively map a pattern-recognition problem to one of higher

dimensionality, e.g. to help separate data into categories. This is

achieved by calculating inner products, as a measure of

coincidence in the data, and eliminates the need to explicitly

represent the data in the higher dimensions.

The pairs of items that constitute a dictionary data structure. The

key is a unique, unmodifiable item that is used to access the

corresponding value.

A simple machine learning algorithm that classifies data by

finding the k nearest neighbours in the feature space,

representing the closest data points with known classification.

The classification is assigned by taking a poll of the classes

represented in the neighbouring points.

A synonym for a self-organising map (see below), named after

Teuvo Kohonen.

With reference to graphical user interfaces, the relative




Likelihood ratio test


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