Python Programming for Biology: Bioinformatics and Beyond



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[Tim J. Stevens, Wayne Boucher] Python Programming

(bioinformatics/graphics):

Retroviruses (biology):

Return (computing):

Return key (computing):

Reverse complement

(molecular biology):

See parallel tempering.

Multiple copies of a simulation or search process that all relate

to the same data, for example so that an optimisation is done

several times in parallel from different starting points.

One of the component monomer chemicals at a particular

position in a biological polymer sequence, i.e. an amino acid at

a location in a polypeptide chain or a nucleotide in a nucleic

acid chain (DNA or RNA).

A measure of the limit in the precision of a measurement, i.e.

what size features can be seen or resolved. With reference to

biomolecular structures the resolution reflects the uncertainty in

the positions of atoms, and depends on the experimental

technique used and the quality of data. When referring to

images the resolution is usually stated simply as the number of

component pixels, often giving width and height separately.

A virus that has an RNA genome, which uses a reverse

transcriptase enzyme to convert the RNA into DNA, the

opposite of the normal biological information flow. The

conversion is often for the purpose of inserting the viral DNA

into the DNA of the host’s genome, a means of lying dormant

and evading the host’s defence mechanisms. HIV, which causes

AIDS, is an example of a retrovirus.

To finish the execution of a function (a subroutine) and pass a

value back to the previous point in the program flow, where the

function was called from.

The key on a keyboard which is used to start a new line or

complete the entry of data. Often synonymous with the Enter

key and frequently symbolised by a bent arrow, going down and

left.


A DNA or RNA sequence that has the opposite kinds of base

and reversed order compared to another sequence, such that the

two nucleic acids could form complementary base pairs, but are

both viewed in the same orientation (usually 5′ to 3′). Given A:T




Ribosome (molecular

biology):

Ribozymes (molecular



biology):

RNA (molecular



biology):

RNA sequence



(molecular biology):

Root (computing):

Root-mean-square

deviation (mathematics):

Rooted tree

(bioinformatics):

and G:C base pairs, the reverse complement of the sequence

ATCCGACTCAG would be CTGAGTCGGAT, so that the first

position for the first sequence pairs with the last position of the

second sequence.

The large enzyme particle inside cells, containing both protein

and RNA, which catalyses the synthesis of new proteins (i.e.

polypeptide chains) by joining individual amino acids (delivered

on a tRNA) and a messenger RNA that specifies the sequence.

Biological catalysts that use RNA to increase the rate of a

reaction, i.e. enzymes that use RNA rather than protein at the

active site.

Ribonucleic acid, biological polymer modules that are copies of

parts of DNA sequences and which have various roles in cells,

including enabling the creation of proteins (transferring DNA

sequence information and delivering amino acids), acting

directly as functional molecules alongside proteins and

controlling the stability of other RNA molecules.

The sequential order of the four different types of nucleotide

compound that make up a linear RNA chain, which is generally

a molecule with a single strand, unlike DNA.

When referring to locations within a file system, the root is the

very top of the containment hierarchy which contains all of the

other sub-directories. On Unix, Linux and Mac OSX-based

systems this is represented with a single forward slash symbol

‘/’. On Windows-based systems there is no single root, rather

there are separate drive letters like ‘C:\’.

A measure of the overall difference between two sets of paired

values. It is calculated as the square root of the average squared

difference between the paired values. Commonly used as a

measure of coordinate difference between three-dimensional

structures.

A hierarchical branching data classification where there is a

base or root. For a phylogenetic tree this means that there is

ancestor node.



Rotation matrix


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