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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

Genomic DNA in Eukaryotes

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.

DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Genome Annotation.

Imad Abugessaisa¹, Takeya Kasukawa¹, Hideya Kawaji^2,3,4

¹Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

Methods in Molecular Biology (Clifton, N.J.)

|November 30, 2016

Summary

This summary is machine-generated.

Genomic annotations reveal genome structure and function, aiding in target identification. This guide explains how to obtain or create these essential genomic data resources.

Keywords:

Epigenetic marks Gene functions Genome annotation Genome browser RNA-Seq

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Genomic research is rapidly advancing, uncovering the dynamic structure and functions of genomes.
Genome annotations, broadly defined as regional characteristics, are crucial for in-depth analysis.
In silico methods for target listing and screening rely heavily on accurate genomic data.

Purpose of the Study:

To provide a comprehensive guide on obtaining and constructing genome annotations.
To offer an overview of available genome annotation types and resources.
To facilitate in silico target identification and screening through accessible genomic data.

Main Methods:

Describing methodologies for accessing publicly available genome annotations.
Outlining procedures for generating custom genome annotations from raw analyses.
Compiling information on diverse genome annotation types and their associated databases.

Main Results:

A clear pathway for acquiring existing genome annotations is presented.
Instructions for building novel genome annotations are detailed.
A catalog of annotation types and relevant resources is provided.

Conclusions:

Genome annotations are fundamental for understanding genome organization and function.
Accessible and well-defined annotations empower advanced genomic analyses, including in silico screening.
This work serves as a practical resource for researchers utilizing genomic data.