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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...

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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Genome Size and the Evolution of New Genes

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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.

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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.

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Genomic Annotation Resources in R/Bioconductor.

Marc R J Carlson^1,2, Hervé Pagès³, Sonali Arora³

¹Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. marc.carlson@seattlechildrens.org.

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

|March 24, 2016

Summary

This summary is machine-generated.

Bioconductor annotation resources are crucial for bioinformatics. This study highlights popular online resources and provides examples for their use in biological data analysis.

Keywords:

Annotation Bioconductor Genomics Next-generation sequencing R

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Bioconductor is a major project providing bioinformatics tools.
Annotation resources are a significant component of Bioconductor.
Numerous online resources are accessible via Bioconductor packages.

Purpose of the Study:

To describe popular Bioconductor annotation resources.
To provide high-level usage examples for these resources.

Main Methods:

Literature review of popular Bioconductor annotation resources.
Illustrative examples of resource access and utilization.

Main Results:

Identification and description of key Bioconductor annotation resources.
Demonstration of practical application through code examples.

Conclusions:

Bioconductor offers valuable annotation resources for biological data.
Understanding and utilizing these resources enhances data analysis workflows.