Related Concept Videos
02:02Genomics
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...
03:36Genome 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.
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
03:00Next-generation Sequencing
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
01:11Genome-wide Association Studies-GWAS
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.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
00:58Genomic 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.
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Introductory Analysis and Validation of CUT&RUN Sequencing Data
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Genomics data resources: frameworks and standards.
1Department of Medical Genetics, University of British Columbia and PI Bioinformatics, Heart + Lung Institute at St. Paul's Hospital, Vancouver, BC, Canada. markw@illuminae.com
Methods in Molecular Biology (Clifton, N.J.)
|March 9, 2012
Summary
Genomics tools have spurred many independent online resources for evolutionary biology. This work explores current approaches and advocates for the Semantic Web as a new standard for data integration.
Area of Science:
- Evolutionary Biology
- Comparative Genomics
- Bioinformatics
Background:
- The rise of genomics tools has led to numerous specialized online resources for evolutionary and comparative biology.
- These resources, including software (WebACT), databases (PaleoDB, GBIF, TreeBase), and ontologies (Evolution Ontology), are largely independent.
- This independence results in incompatible technologies and fragmented data access for the scientific community.
Purpose of the Study:
- To explore existing and emerging approaches for online resource publication in evolutionary and comparative biology.
- To analyze the strengths and weaknesses of various data and tool provision frameworks.
- To lay the groundwork for the Semantic Web as a potential global standard for biodiversity data integration.
Main Methods:
- Review and analysis of current online resource publication approaches in evolutionary biology.
- Exploration of informatics theories and philosophies behind different frameworks.
- Discussion of the potential of the Semantic Web for data and knowledge representation.
Main Results:
- Identification of a myriad of independent and often incompatible online resources.
- Evaluation of the limitations of current decentralized approaches to data sharing.
- Highlighting the potential of the Semantic Web to address data discovery and integration challenges.
Conclusions:
- The current landscape of online resources in evolutionary biology is fragmented due to independent development.
- The Semantic Web offers a promising framework for a unified approach to biodiversity data and knowledge representation.
- Adoption of new standards like the Semantic Web is crucial for improving data accessibility and integration.