Genomics is the study of an organism's entire genome.

Investigation of single genes,

their functions and roles is something very common in today's medical and biological
research, and can not be said to be genomics but rather the most typical feature of
molecular biology.

Genomics can be said to have appeared in the 1980s, and took off in the 1990s with the
initiation of genome projects for several species. A major branch of genomics is still
concerned with sequencing the genomes of various organisms, although the knowledge of
full genomes have created the possibility for the field of functional genomics, mainly
concerned with patterns of gene expression during various conditions. The most
important tools here are microarrays and bioinformatics.

Proteomics is the large-scale study of protein, particularly their structures and functions.
It is also the study of the full set of proteins in a cell type or tissue, and the changes
during various conditions. This term was coined to make an analogy with genomics, and
while it is often viewed as the "next step", proteomics is much more complicated than
genomics. Most importantly, while the genome is a rather constant entity, the proteome
differs from cell to cell and is constantly changing through its biochemical interactions
with the genome and the environment. One organism has radically different protein
expression in different parts of its body, in different stages of its life cycle and in different
environmental conditions.

The word is derived from PROTEins and by genOME, since proteins are expressed by
the genome. The proteome refers to all the proteins produced by an organism, much like
the genome is the entire set of genes. The human body may contain more than 2 million
different proteins, each having different functions. Thus, proteomics is the study of the
composition, structure, function, and interaction of the proteins directing the activities of
each living cell. As the main components of the physiological pathways of the cells,
proteins serve as vital functions in the body.

Comparative genomics is the study of relationships between the genomes of different

species or strains. Comparative genomics is an attempt to take advantage of the
information provided by the signatures of selection to understand the function and
evolutionary processes that act on genomes. While it is still a young field, it holds great
promise to yield insights into many aspects of the evolution of modern species. The sheer
amount of information contained in modern genomes (several gigabytes in the case of
humans) necessitates that the methods of comparative genomics are mostly
computational in nature. Gene finding is an important application of comparative
genomics, as is discovery of new, non-coding functional elements of the genome.

Comparative genomics exploits both similarities and differences in the proteins, RNA,
and regulatory regions of different organisms to infer how selection has acted upon these
elements. Those elements that are responsible for similarities between different species
should be conserved through time (stabilizing selection), while those elements
responsible for differences among species should be divergent (positive selection).
Finally, those elements that are unimportant to the evolutionary success of the organism
will be unconserved (selection is neutral).

Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is

one of the important goals of the field. It is however often complicated by the multiplicity
of events that have taken place throughout the history of individual lineages, leaving only
distorted and superimposed traces in the genome of each living organism. For this reason
comparative genomics studies of small model organisms (for example yeast) are of great
importance to advance our understanding of general mechanisms of evolution.

Having come a long way from its initial use of finding functional proteins, comparative
genomics is now concentrating on finding regulatory regions and siRNA molecules.
Recently, it has been discovered that distantly related species often share long conserved
stretches of DNA that do not appear to code for any protein. It is unknown at this time
what function such ultra-conserved regions serve.

The goal of comparative proteomics is to systematically compare global protein

expression profiles, focusing on quantitative changes that occur as a function of disease,
treatment or environment (Somiari et al.,
2003).Such an approach may provide comprehensive insight into the dynamics of the
proteome and reveal protein markers of disease. The increasing volume of data from
high-throughput proteomics urgently needs to be made accessible in databases with
standards for data storage, exchange and analysis.
Comparative proteomics may be helpful to shorten the transfer between model and
agronomic target species. Comparative proteomics has been used with the long-term goal
to locate, detect, and characterize the differentially expressed proteins (DEPs) in human
pituitary adenomas; to identify tumor-related and -specific biomarkers; and to clarify the
basic molecular mechanisms of pituitary adenoma formation.

Drug design is the approach of finding drugs by design, based on their biological targets.
Typically a drug target is a key molecule involved in a particular metabolic or signaling
pathway that is specific to a disease condition or pathology, or to the infectivity or
survival of a microbial pathogen.
Some approaches attempt to stop the functioning of the pathway in the diseased state by
causing a key molecule to stop functioning. Drugs may be designed that bind to the active
region and inhibit this key molecule. However these drugs would also have to be
designed in such a way as not to affect any other important molecules that may be similar
in appearance to the key molecules. Sequence homologies are often used to identify such
risks.

Other approaches may be to enhance the normal pathway by promoting specific

molecules in the normal pathways that may have been affected in the diseased state.

The structure of the drug molecule that can specifically interact with the biomolecules
can be modeled using computational tools. These tools can allow a drug molecule to be
constructed within the biomolecule using knowledge of its structure and the nature of its
active site. Construction of the drug molecule can be made inside out or outside in
depending on whether the core or the R-groups are chosen first. However many of these
approaches are plagued by the practical problems of chemical synthesis.

Newer approaches have also suggested the use of drug molecules that are large and
proteinaceous in nature rather than as small molecules. There have also been suggestions
to make these using mRNA. Gene silencing may also have therapeutical applications.

There are over 1,000 public and commercial biological databases. These biological
databases usually contain genomics and proteomics data, but databases are also used in
taxonomy. The data are nucleotide sequences of genes or amino acid sequences of
proteins. Biological databases have become an important tool in assisting scientists to
understand and explain a host of biological phenomena from the structure of
biomolecules and their interaction, to the whole metabolism of organisms and to
understanding the evolution of species. This knowledge helps facilitate the fight against
diseases, assists in the development of medications and in discovering basic relationships
amongst species in the history of life.

The biological knowledge of databases is usually (locally) distributed amongst many

different specialized databases. This makes it difficult to ensure the consistency of
information, which sometimes leads to low data quality.

By far the most important resource for biological databases is a special (yearly) issue of
the journal "Nucleic Acids Research" (NAR). The Database Issue is freely available, and
categorizes all the publicly available online databases related to computational biology
(or bioinformatics).
The term "sequence analysis" in biology implies subjecting a DNA or peptide sequence
to sequence alignment, sequence databases, repeated sequence searches, or other
bioinformatics methods on a computer.

Sequence analysis in molecular biology and bioinformatics is an automated, computer-

based examination of characteristical fragments, e.g. of a DNA-strand. It basically
includes five biologically relevant topics:

1. the comparison of sequences in order to find similar sequences (sequence

alignment)
2. identification of gene-structures, reading frames, distributions of introns and
exons and regulatory elements
3. prediction of protein structures
4. genome mapping
5. comparison of homologous sequences to construct a molecular phylogeny

In chemistry, sequence analysis comprises techniques used to do determine the sequence

of a polymer formed of several monomers. In molecular biology and genetics, the same
process is called simply "sequencing."

In biology, phylogenetics (Greek: phylon = tribe, race and genetikos = relative to birth,
from genesis = birth) is the study of evolutionary relatedness among various groups of
organisms (e.g., species, populations). Also known as phylogenetic systematics,
phylogenetics treats a species as a group of lineage-connected individuals over time.
Phylogenetic taxonomy, which is an offshoot of, but not a logical consequence of,
phylogenetic systematics, constitutes a means of classifying groups of organisms
according to degree of evolutionary relatedness.

Phylogeny (or phylogenesis) is the origin and evolution of a set of organisms, usually a
set of species. A major task of systematics is to determine the ancestral relationships
among known species (both living and extinct). The most commonly used methods to
infer phylogenies include parsimony, maximum likelihood, and MCMC-based Bayesian
inference. Distance-based methods construct trees based on overall similarity which is
often assumed to approximate phylogenetic relationships. All methods depend upon an
implicit or explicit mathematical model describing the evolution of characters observed
in the species included, and are usually used for molecular phylogeny where the
characters are aligned nucleotide or amino acid sequences.
Molecular dynamics (MD) is a form of computer simulation where atoms and molecules
are allowed to interact for a period of time under known laws of physics. Because in
general molecular systems consist of a large number of particles, it is impossible to find
the properties of such complex systems analytically. MD simulation circumvents this
problem by using numerical methods. It represents an interface between laboratory
experiments and theory and can be understood as a virtual experiment.

Even though we know matter consists of interacting particles in motion at least since
Boltzmann in the 19th Century, many still think of molecules as rigid museum models.
Richard Feynman said in 1963 that "everything that living things do can be understood in
terms of the jiggling and wiggling of atoms." [1] One of MD's key contributions is creating
awareness that molecules like proteins and DNA are machines in motion. [2] MD probes
the relationship between molecular structure, movement and function.

Molecular dynamics is a multidisciplinary field. Its laws and theories stem from
mathematics, physics and chemistry. MD employs algorithms from computer science and
information theory. It was originally conceived within theoretical physics in the 1950's,
but is applied today mostly in materials science and biomolecules.

Subdiscipline of bioinformatics that focuses on the representation, storage, retrieval,

analysis and display of structural information at the atomic and subcellular spatial scales.
Structural Biological Analysis can provide the ultimate insight into the mechanism
behind a biological function, understand how biological function follows structure.

• Goals
– Creation of methods for manipulating structural data
– Application of these methods to solving problems in biology and discovery of new
patterns.