|
Bioinformatics Glossary
Part:
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
(Continued from previous part...)
Rational drug design (Structure based drug design)
The development of drugs based on the 3-dimensional molecular structure
of a particular target.
Reading frame
A sequence of codons beginning with an intiation codon and ending with
a termination codon, typically of at least 150 bases (50 amino acids) coding
for a polypeptide or protein chain (see ORF and URF).
Reagents
Sources of biological or chemical material that can be used as the starting
blocks in laboratory experiments. Reagents can range from chemicals needed
to perform a particular chemical reaction, constituents of a laboratory
protocol, or clones to be used in a large-scale gene expression study.
Recessive
Any trait that is expressed phenotypically only when present on both
alleles of a gene (cf dominant).
Recombinant DNA (rDNA)
DNA molecules resulting from the fusion of DNA from different sources.
The technology employed for splicing DNA from different sources and for
amplifying the resultant heterogenous DNA.
Recombination
A new combination of alleles resulting from the rearrangement occuring
by crossing-over or by independent assortment (see crossing over).
Recursion
An algorithmic procedure whereby an algorithm calls on itself to perform
a calculation until the result exceeds a threshold, in which case the algorithm
exits. Recursion is a powerful procedure with which to process data and
is computationally quite efficient.
Regulatory gene
A DNA sequence that functions to control the expression of other genes
by producing a protein that modulates the synthesis of their products (typically
by binding to the gene promoter). (cf. Structural gene).
Relational Database
A database that follows E. F. Codd’s 11 rules, a series of mathematical
and logical steps for the organization and systemization of data into a
software system that allows easy retrieval, updating, and expansion. An
RDBMS stores data in a database consisting of one or more tables of rows
and columns. The rows correspond to a record (tuple); the columns correspond
to attributes (fields) in the record. In an RDBMS, a view, defined as a
subset of the database that is the result of the evaluation of a query,
is a table. RDBMSs use Structured Query Language (SQL) for data definition,
data management, and data access and retrieval. Relational and object-relational
databases are used extensively in bioinformatics to store sequence and
other biological data.
Relational Database Management Systems (RDBMS)
A software system that includes a database architecture, query language,
and data loading and updating tools and other ancillary software that together
allow the creation of a relational database application.
Repeats (repeat sequences)
Repeat sequences and approximate repeats occur throughout the DNA of
higher organisms (mammals). For example, the Alu sequences of length
about 300 characters, appear hundreds of thousands of times in Human DNA
with about 87% homology to a consensus Alu string. Some short substrings
such as TATA-boxes, poly-A and (TG)* also appear more often than by chance.
Repeat sequences may also occur within genes, as mutations or alterations
to those genes. Repetitive sequences, especially mobile elements, have
many applications in genetic research. DNA transposons and retroposons
are routinely used for insertional mutagenesis, gene mapping, gene tagging,
and gene transfer in several model systems.
Repetitive elements
Repetitive elements provide important clues about chromosome dynamics,
evolutionary forces, and mechanisms for exchange of genetic information
between organisms The most ubiquitous class of repetitive elements in the
DNA sequence in primate genomes is the Alu family of interspersed
repeats which have arisen in the last 65 million years of evolution Alu
repeats belong to a class of sequences defined as short interspersed elements
(SINEs). Approximately 500,000 Alu SINEs exist within the human
genome, representing about 5% of the genome by mass.
Replication
The synthesis of an informationally identical macromolecule (e.g. DNA)
from a template molecule.
Repressor
The protein product of a regulatory gene that combines with a specific
operator (regulatory DNA sequence) and hence blocks the transcription of
genes in an operon.
Restriction enzyme (restriction endonuclease)
A type of enzyme that recognizes specific DNA sequences (usually palindromic
sequences 4, 6, 8 or 16 base pairs in length) and produces cuts on both
strands of DNA containing those sequences only. The "molecular scissors"
of rDNA technology.
Restriction fragment length polymorphisms (RFLPs)
Variation within the DNA sequences of organisms of a given species that
can be identified by fragmenting the sequences using restriction enzymes,
since the variation lies within the restriction site. RFLPs can be used
to measure the diversity of a gene in a population.
Restriction map
A physical map or depiction of a gene (or genome) derived by ordering
overlapping restriction fragments produced by digestion of the DNA with
a number of restriction enzymes.
Reverse Genetics
The use of protein information to elucidate the genetic sequence encoding
that protein. Used to describe the process of gene isolation starting with
a panel of afflicted patients (see positional cloning).
Reverse transcriptase
A DNA polymerase that can synthesise a complementary DNA (cDNA) strand
using RNA as a template - a so-called RNA-dependent DNA polymerase.
Reverse transcriptase-PCR (RT-PCR)
Procedure in which PCR amplification is carried out on DNA that is first
generated by the conversion of mRNA to cDNA using reverse transcriptase.
Ribonucleic acid (RNA)
A category of nucleic acids in which the component sugar is ribose and
consisting of the four nucleotides Thymidine, Uracil, Guanine, and Adenine.
The three types of RNA are messenger RNA (mRNA), transfer RNA (tRNA) and
ribosomal RNA (rRNA).
(Continued on next part...)
Part:
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
| 