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

Restriction Enzymes01:11

Restriction Enzymes

Restriction enzymes are bacterial enzymes used to cut DNA in a sequence-specific manner. To cleave DNA, they bind to specific palindromic sequences called restriction sites. Such palindromic DNA sequences or inverted repeats are commonly found in regions of functional significance, such as the origin of replication, gene operator sites, and regions containing transcription termination signals.
The host bacteria protect their own genomic DNA from these enzymes by methylating these sites. Some...
DNA Isolation01:24

DNA Isolation

DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...

You might also read

Related Articles

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

Sort by
Same author

The effects of K+ channel blockers on the spontaneous electrical and contractile activity in the proximal renal pelvis of the guinea pig.

The Journal of urology·1996
Same author

Interferon-gamma inhibits HIV-induced invasiveness of monocytes.

Journal of leukocyte biology·1995
Same author

Phosphorylation of Raf by ceramide-activated protein kinase.

Nature·1995
Same author

Cyclin D3 is essential for megakaryocytopoiesis.

Blood·1995
Same author

A P2X purinoceptor cDNA conferring a novel pharmacological profile.

FEBS letters·1995
Same author

Phosphorylation of nodulin 26 on serine 262 affects its voltage-sensitive channel activity in planar lipid bilayers.

The Journal of biological chemistry·1995
Same journal

In silico analysis, annotation and characterisation of putative ESTs from Sorghum bicolor associated with heat stress.

International journal of bioinformatics research and applications·2015
Same journal

Docking analysis of gallic acid derivatives as HIV-1 protease inhibitors.

International journal of bioinformatics research and applications·2015
Same journal

Automatic segmentation of Potyviridae family polyproteins.

International journal of bioinformatics research and applications·2015
Same journal

Neural network and rough set hybrid scheme for prediction of missing associations.

International journal of bioinformatics research and applications·2015
Same journal

On the interconnection of stable protein complexes: inter-complex hubs and their conservation in Saccharomyces cerevisiae and Homo sapiens networks.

International journal of bioinformatics research and applications·2015
Same journal

Diversity and evolution of the envelope gene of dengue virus type 1 circulating in India in recent times.

International journal of bioinformatics research and applications·2015
See all related articles

Related Experiment Video

Updated: Jun 28, 2026

Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector
12:08

Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector

Published on: March 28, 2018

Solving large double digestion problems for DNA restriction mapping by using branch-and-bound integer linear

Z Wu1, Y Zhang

  • 1Department of Mathematics, Iowa State University, Ames, Iowa 50011, USA. zhijun@iastate.edu

International Journal of Bioinformatics Research and Applications
|November 15, 2008
PubMed
Summary
This summary is machine-generated.

Solving the complex DNA restriction mapping problem is now feasible for larger datasets. This study presents a novel mixed-integer linear program formulation, enabling efficient computation for previously intractable DNA fragment analysis.

More Related Videos

A Universal Protocol for Large-scale gRNA Library Production from any DNA Source
10:32

A Universal Protocol for Large-scale gRNA Library Production from any DNA Source

Published on: December 6, 2017

Associated Chromosome Trap for Identifying Long-range DNA Interactions
14:49

Associated Chromosome Trap for Identifying Long-range DNA Interactions

Published on: April 23, 2011

Related Experiment Videos

Last Updated: Jun 28, 2026

Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector
12:08

Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector

Published on: March 28, 2018

A Universal Protocol for Large-scale gRNA Library Production from any DNA Source
10:32

A Universal Protocol for Large-scale gRNA Library Production from any DNA Source

Published on: December 6, 2017

Associated Chromosome Trap for Identifying Long-range DNA Interactions
14:49

Associated Chromosome Trap for Identifying Long-range DNA Interactions

Published on: April 23, 2011

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Genomics

Background:

  • The DNA restriction mapping problem, specifically double digestion, is computationally challenging (NP-complete).
  • Existing methods are effective only for small numbers of DNA fragments.
  • Large-scale DNA analysis requires more scalable computational approaches.

Purpose of the Study:

  • To develop a more efficient computational method for DNA restriction mapping.
  • To address the intractability of the double digestion problem for large DNA fragment sets.
  • To improve the scalability of DNA fragment analysis.

Main Methods:

  • Formulating the DNA restriction mapping problem as a mixed-integer linear program (MIP).
  • Utilizing advanced integer programming techniques for problem-solving.
  • Testing the formulation with randomly generated large-scale problems.

Main Results:

  • The MIP formulation successfully addresses the double digestion problem.
  • The approach significantly expands the solvable problem size compared to previous methods.
  • Randomly generated problems with vastly larger search spaces were efficiently solved.

Conclusions:

  • The proposed MIP formulation offers a scalable solution for DNA restriction mapping.
  • State-of-the-art integer programming techniques make large-scale DNA fragment analysis tractable.
  • This method advances computational approaches in bioinformatics and genomics.