Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Maxam-Gilbert Sequencing01:05

Maxam-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...
Sanger Sequencing01:57

Sanger 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...
RNA-seq03:21

RNA-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...
Next-generation Sequencing03:00

Next-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.
Genome Annotation and Assembly03:36

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.
Synthetic Biology02:55

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Biodegradation and chiral stability of fipronil in aerobic and flooded paddy soils.

The Science of the total environment·2008
Same author

Dietary risk assessment of spinosad in China.

Regulatory toxicology and pharmacology : RTP·2007
Same author

Risk assessment of lambda-cyhalothrin on aquatic organisms in paddy field in China.

Regulatory toxicology and pharmacology : RTP·2007
Same author

The status of electronic laboratory notebooks for chemistry and biology.

Current opinion in drug discovery & development·2006
Same author

VET: a tool for reaction plausibility checking.

Journal of chemical information and modeling·2006
Same author

Reoptimization of MDL keys for use in drug discovery.

Journal of chemical information and computer sciences·2002
Same journal

Advancing Biochemical Molecule Registration, Representation and Search for New Drug Modalities.

Journal of chemical information and modeling·2026
Same journal

A Unified Molecular Graph and Protein Language Model Framework for Predicting Human Drug-Hormone Receptor Interactions with Structure-Aware Validation.

Journal of chemical information and modeling·2026
Same journal

Intricate Role of Cholesterol in Membrane Fusion.

Journal of chemical information and modeling·2026
Same journal

tmGNN-XAI: An Explainable Graph Neural Network Tool for Predicting Electronic Properties of Transition Metal Complexes from SMILES.

Journal of chemical information and modeling·2026
Same journal

QSAR in the Browser: An Interactive Cheminformatics Web Application.

Journal of chemical information and modeling·2026
Same journal

FoldDoF: Utilizing the Primary Degrees of Freedom of Protein Backbone for Geometric Modeling and Generation.

Journal of chemical information and modeling·2026
See all related articles

Related Experiment Video

Updated: May 30, 2026

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling
08:04

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

Published on: October 8, 2019

Self-contained sequence representation: bridging the gap between bioinformatics and cheminformatics.

William L Chen1, Burton A Leland, Joseph L Durant

  • 1Accelrys, Incorporated, San Ramon, California 94583, United States. williamlingran.chen@accelrys.com

Journal of Chemical Information and Modeling
|August 2, 2011
PubMed
Summary
This summary is machine-generated.

A new Self-Contained Sequence Representation (SCSR) addresses challenges in managing biopolymer data. This compressed format integrates bioinformatics and cheminformatics, enabling advanced sequence searching and data handling.

More Related Videos

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Related Experiment Videos

Last Updated: May 30, 2026

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling
08:04

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

Published on: October 8, 2019

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Bioinformatics and Cheminformatics
  • Computational Biology
  • Data Management

Background:

  • Next-generation sequencing generates vast amounts of data, posing challenges for bioinformatics.
  • Managing biomacromolecules at the chemical level is difficult due to a lack of suitable biopolymer representations in cheminformatics.

Purpose of the Study:

  • Introduce the Self-Contained Sequence Representation (SCSR) for biopolymers.
  • Combine strengths of bioinformatics and cheminformatics notations.
  • Provide a compressed, chemically detailed representation for biopolymers.

Main Methods:

  • Developed SCSR as a general, extensible, and comprehensive biopolymer representation.
  • Enhanced the molfile format to support SCSR.
  • Created SCSR-based exact structure and substructure searching methods (NEMA key and SSS).

Main Results:

  • SCSR offers a compressed format retaining detailed chemical information for biopolymers.
  • SCSR enables high-performance exact structure and substructure searching.
  • The molfile format now supports SCSR, facilitating its integration.

Conclusions:

  • SCSR provides a robust framework for managing and handling sequence data at the chemical level.
  • SCSR lays the foundation for integrating bioinformatics and cheminformatics.
  • SCSR enhances biopolymer data analysis and retrieval capabilities.