Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes—according to Wikipedia’s definition. Wikipedia further elaborates on genomics as the following.
A genome is an organism’s complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration.
In contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism’s genes, their interrelations and influence on the organism.
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Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells.
Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes.
Advances in genomics have triggered a revolution in discovery-based research and systems biology to facilitate understanding of even the most complex biological systems such as the brain.
The genomics field also includes studies of intragenomic (within the genome) phenomena such as epistasis (effect of one gene on another), pleiotropy (one gene affecting more than one trait), heterosis (hybrid vigour), and other interactions between loci and alleles within the genome.
In genome analysis, after an organism has been selected, genome projects involve three components: the sequencing of DNA, the assembly of that sequence to create a representation of the original chromosome, and the annotation and analysis of that representation.
Genome sequencing approaches fall into two broad categories, shotgun and high-throughput (or next-generation) sequencing.
Genome sequence assembly refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence. This is needed as current DNA sequencing technology cannot read whole genomes as a continuous sequence, but rather reads small pieces of between 20 and 1000 bases, depending on the technology used.
Genome sequence assembly can be broadly categorized into two approaches: de novo assembly, for genomes which are not similar to any sequenced in the past, and comparative assembly, which uses the existing sequence of a closely related organism as a reference during assembly.
Finished genomes are defined as having a single contiguous sequence with no ambiguities representing each replicon.
The DNA sequence assembly alone is of little value without additional analysis. Genome annotation is the process of attaching biological information to sequences, and consists of three main steps. One, identifying portions of the genome that do not code for proteins; two, identifying elements on the genome, a process called gene prediction; three, attaching biological information to these elements. Automatic annotation tools try to perform these steps in silico, as opposed to manual annotation (a.k.a. curation) which involves human expertise and potential experimental verification. Ideally, these approaches co-exist and complement each other in the same annotation pipeline.
Sequencing pipelines and databases. The need for reproducibility and efficient management of the large amount of data associated with genome projects mean that computational pipelines have important applications in genomics.
Research areas of genomics are functional genomics, structural genomics, epigenomics, metagenomics, model systems, viruses and bacteriophages, and cyanobacteria.
Applications of genomics are genomic medicine, synthetic biology and bioengineering, and population and conservation genomics.
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