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Redundancy:

Redundancy means having more than one equivalent OR More than one
codon specifies individual amino acids

Degeneracy is the redundancy of the genetic code. This term was given by
Bernfield and Nirenberg. The genetic code has redundancy but no ambiguity
(see the codon tables below for the full correlation). For example, although
codons GAA and GAG both specify glutamic acid (redundancy), neither
specifies another amino acid (no ambiguity). The codons encoding one
amino acid may differ in any of their three positions. For example, the amino
acid leucine is specified by YUR or CUN (UUA, UUG, CUU, CUC, CUA, or CUG)
codons (difference in the first or third position indicated using IUPAC
notation), while the amino acid serine is specified by UCN or AGY (UCA, UCG,
UCC, UCU, AGU, or AGC) codons. A practical consequence of redundancy is
that errors in the third position of the triplet codon cause only a silent
mutation or an error that would not affect the protein because the
hydrophilicity or hydrophobicity is maintained by equivalent substitution of
amino acids; for example, a codon of NUN (where N = any nucleotide) tends
to code for hydrophobic amino acids. NCN yields amino acid residues that are
small in size and moderate in hydropathy; NAN encodes average size
hydrophilic residuesThe genetic code is so well-structured for hydropathy
that a mathematical analysis (Singular Value Decomposition) of 12 variables
(4 nucleotides x 3 positions) yields a remarkable correlation (C = 0.95) for
predicting the hydropathy of the encoded amino acid directly from the triplet
nucleotide sequence, without translation. Note in the table, below, eight
amino acids are not affected at all by mutations at the third position of the
codon, whereas in the figure above, a mutation at the second position is
likely to cause a radical change in the physicochemical properties of the
encoded amino acid.

Ontology:
Ontology is an organizational system designed to categorize and help explain
the relationships between various concepts of science in the same area of
knowledge and research.

Functions of Ontology:
It provides a common background and understanding of a particular
domain, or field, of study, and ensures a common ground among those
who study the information.
It is a way of organizing concepts, information, and ideas that is meant
to be universal within the field, and allows for a common language to
be spoken.
It is a structural framework that allows the concepts to be laid out in a
way that makes sense.
It helps show the connections and relationships between concepts in a
manner that is generally accepted by the field.

An example of ontology is when a physicist establishes different categories


to divide existing things into in order to better understand those things and
how they fit together in the broader world

Gene bank statistics:

Gene bank WGS


Release Date Bases Sequences Bases
Sequences

200 Feb 2014 157943793171 171123749 591378698544


139725795
201 Apr 2014 159813411760 171744486 621015432437
143446790
202 Jun 2014 161822845643 173353076 719581958743
175779064
203 Aug 2014 165722980375 174108750 774052098731
189080419
204 Oct 2014 181563676918 178322253 805549167708
196049974
205 Dec 2014 184938063614 179295769 848977922022
200301550
206 Feb 2015 187893826750 181336445 873281414087
205465046
207 Apr 2015 189739230107 182188746 969102906813
243779199
208 Jun 2015 193921042946 185019352 1038937210221
258702138
209 Aug 2015 199823644287 187066846 1163275601001
302955543
210 Oct 2015 202237081559 188372017 1222635267498
309198943
211 Dec 2015 203939111071 189232925 1297865618365
317122157
212 Feb 2016 207018196067 190250235 1399865495608
333012760
213 Apr 2016 211423912047 193739511 1452207704949
338922537
214 Jun 2016 213200907819 194463572 1556175944648
350278081
215 Aug 2016 217971437647 196120831 1637224970324
359796497
216 Oct 2016 220731315250 197390691 1676238489250
363213315
217 Dec 2016 224973060433 198565475 1817189565845
395301176
218 Feb 2017 228719437638 199341377 1892966308635
409490397

Genome pharmacology:
Pharmacogenomics is the study of the role of the genome in drug response.
Its name (pharmaco- + genomics) reflects its combining of pharmacology
and genomics. Pharmacogenomics can be defined as the technology that
analyzes how the genetic makeup of an individual affects his/her response to
drugs. It deals with the influence of acquired and inherited genetic variation
on drug response in patients by correlating gene expression or single-
nucleotide polymorphisms with pharmacokinetics and pharmacodynamics
(drug absorption, distribution, metabolism, and elimination), as well as drug
receptor target effects. The term pharmacogenomics is often used
interchangeably with pharmacogenetics. Although both terms relate to drug
response based on genetic influences, pharmacogenetics focuses on single
drug-gene interactions, while pharmacogenomics encompasses a more
genome-wide association approach, incorporating genomics and epigenetics
while dealing with the effects of multiple genes on drug response.

Entrez

PubMed query:

papers databases pubmed


hemoglobin
Human hemoglobin
Human hemoglobin 34 3709
AND structure
Human hemoglobin
AND function
Hemoglobin [TI]
Human hemoglobin
[AB]
Human hemoglobin [TI]
AND structure [TIAB]
Human Hemoglobin [TI]
and structure [TIAB]
AND function [TIAB]
Hemoglobin [TI] OR
haemoglobin [TI] AND
structure [TIAB]

Sodmergen
Danchin
Danchin A
Li
Li Y
LiYX
Smith
Smith T

rice
rice [TI]
rice [AU]
rice [AU] AND rice

rice
Oryza sativa
rice OR Oryza sativa

Luo J
Luo JC
Luo J [AU] AND
BIOINFORMATICS
Luo J [AU] AND Peking
University [AD]
Luo J [AU] AND Peking
University [AD] AND
(bioinformatics OR
database OR rice)