Related Concept Videos
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.
03:21RNA-seq
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
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...
01:57Sanger Sequencing
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
01:05Maxam-Gilbert Sequencing
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
Challenges of the Maxam-Gilbert Method
The...
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Related Experiment Video
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09:14
Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
Published on: June 28, 2018
Extending KNIME for next-generation sequencing data analysis.
Bernd Jagla1, Bernd Wiswedel, Jean-Yves Coppée
1Departement Génomes et Génétique, Institut Pasteur, Plate-forme Transcriptome et Epigénome, 25 Rue du Docteur Roux, F-75015 Paris, France. bernd.jagla@pasteur.fr
Bioinformatics (Oxford, England)
|August 30, 2011
Summary
KNIME, a user-friendly platform, now offers new functionality for next-generation sequencing analysis. This open-source tool enhances data integration, processing, and exploration for researchers.
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Published on: April 11, 2016
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- KNIME (Konstanz Information Miner) is an established open-source platform for data integration, processing, analysis, and exploration.
- Next-generation sequencing (NGS) generates vast amounts of biological data requiring sophisticated analytical tools.
Purpose of the Study:
- To introduce new functionalities and workflows within the KNIME framework specifically designed for next-generation sequencing analysis.
- To enable researchers to perform complex NGS analyses using a user-friendly, integrated platform.
Main Methods:
- Development of new modules and workflows within the KNIME analytics platform.
- Integration of existing bioinformatics tools and algorithms into the KNIME environment.
- Creation of example workflows for common NGS analysis tasks.
Main Results:
- Successful implementation of novel functionalities for NGS data analysis in KNIME.
- Demonstration of the platform's capability to handle complex NGS workflows.
- Availability of example workflows and comprehensive documentation.
Conclusions:
- KNIME provides a powerful, user-friendly, and comprehensive open-source solution for next-generation sequencing analysis.
- The presented enhancements significantly expand the utility of KNIME for genomic research.
- Researchers can leverage these new capabilities for efficient and effective NGS data exploration and processing.