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

Gap Junctions01:37

Gap Junctions

57.0K
Multicellular organisms employ a variety of ways for cells to communicate with each other. Gap junctions are specialized proteins that form pores between neighboring cells in animals, connecting the cytoplasm between the two, and allowing for the exchange of molecules and ions. They are found in a wide range of invertebrate and vertebrate species, mediate numerous functions including cell differentiation and development, and are associated with numerous human diseases, including cardiac and...
57.0K
Impression Management Techniques III: Aligning Actions01:29

Impression Management Techniques III: Aligning Actions

127
Aligning actions are communicative strategies individuals employ to maintain social harmony and preserve personal identity in the face of potential disruptions to social norms. These actions are particularly important in managing social impressions when one's behavior might be seen as inappropriate, incompetent, or morally questionable.Types of Aligning ActionsThe three principal types of aligning actions are disclaimers, accounts, and apologies.DisclaimersDisclaimers are preventive; they are...
127
Design Example: Alignment of a Road Line Using GIS01:17

Design Example: Alignment of a Road Line Using GIS

339
The alignment of a road line using Geographic Information Systems (GIS) is a critical process in civil engineering, combining advanced technology with practical decision-making. This methodology begins with the collection of geospatial data, including information on land cover, geomorphology, drainage patterns, slope, and contour details. Such data is typically acquired through satellite imagery and GIS tools, offering a comprehensive understanding of the terrain.Once the data is gathered, it...
339
Gap Junctions01:27

Gap Junctions

9.4K
The cytoplasm of adjacent animal cells can exchange small molecules, ions, and secondary messengers via the communication channels which form the gap junctions. These junctions comprise a few hundred to thousands of molecular channels, each made of two halves, called the connexon hemichannel. A connexon is a hexamer of six transmembrane connexin proteins, which assemble radially, thus forming a pore or channel in the center. One connexon hemichannel docks with a corresponding connexon on the...
9.4K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

11.6K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
11.6K
Sanger Sequencing01:57

Sanger Sequencing

773.7K
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...
773.7K

You might also read

Related Articles

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

Sort by
Same author

Efficacy and Toxicity of Stereotactic Body Radiotherapy for Early to Advanced Stage Hepatocellular Carcinoma - Initial Experience From an Australian Liver Cancer Service.

Clinical oncology (Royal College of Radiologists (Great Britain))·2020
Same author

Hepatic gene expression variations in response to high-fat diet-induced impaired glucose tolerance using RNAseq analysis in collaborative cross mouse population.

Mammalian genome : official journal of the International Mammalian Genome Society·2019
Same author

Magneto-optic trap using a reversible, solid-state alkali-metal source.

Optics letters·2019
Same author

Integration of Murine and Human Studies for Mapping Periodontitis Susceptibility.

Journal of dental research·2018
Same author

Maximum-likelihood estimation of the statistical distribution of Smith-Waterman local sequence similarity scores.

Bulletin of mathematical biology·2015
Same author

Carcinoid tumor of the lung metastatic to a previously identified pituitary adenoma.

Journal of surgical case reports·2014

Related Experiment Video

Updated: Jan 22, 2026

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

3.2K

Local sequence alignments with monotonic gap penalties.

R Mott1

  • 1SmithKline-Beecham Pharmaceuticals R & D, New Frontiers Science Park (North),3rd Avenue, Harlow CM19 5AW, UK. Richard.Mott@well.ox.ac.uk

Bioinformatics (Oxford, England)
|June 26, 1999
PubMed
Summary

This study introduces a new dynamic programming algorithm for sequence alignment that uses non-linear gap penalties. This approach improves the detection of biological similarities, especially those involving long gaps.

More Related Videos

Identification of Plasmodesmal Localization Sequences in Proteins In Planta
08:07

Identification of Plasmodesmal Localization Sequences in Proteins In Planta

Published on: August 15, 2017

8.7K
Analysis of Protein-protein Interactions and Co-localization Between Components of Gap, Tight, and Adherens Junctions in Murine Mammary Glands
11:31

Analysis of Protein-protein Interactions and Co-localization Between Components of Gap, Tight, and Adherens Junctions in Murine Mammary Glands

Published on: May 30, 2017

10.4K

Related Experiment Videos

Last Updated: Jan 22, 2026

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

3.2K
Identification of Plasmodesmal Localization Sequences in Proteins In Planta
08:07

Identification of Plasmodesmal Localization Sequences in Proteins In Planta

Published on: August 15, 2017

8.7K
Analysis of Protein-protein Interactions and Co-localization Between Components of Gap, Tight, and Adherens Junctions in Murine Mammary Glands
11:31

Analysis of Protein-protein Interactions and Co-localization Between Components of Gap, Tight, and Adherens Junctions in Murine Mammary Glands

Published on: May 30, 2017

10.4K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Traditional sequence alignment methods using affine gap penalties can inaccurately penalize long gaps, potentially missing biologically relevant similarities.
  • There is a need for efficient algorithms capable of handling non-linear gap penalties for more accurate local sequence alignments.

Purpose of the Study:

  • To develop and describe an efficient dynamic programming algorithm for computing optimal local sequence alignments with arbitrary, monotonically increasing gap penalties.
  • To demonstrate the advantage of non-affine gap penalties in detecting sequence similarities that include long gaps.

Main Methods:

  • A novel dynamic programming algorithm is presented for optimal local sequence alignment.
  • The algorithm accommodates monotonically increasing gap penalties, where the cost of a gap increases with its length.
  • Computational complexity analysis is provided, with optimizations discussed to improve performance.

Main Results:

  • The algorithm achieves an expected running time of O(mn) under typical scoring schemes, with a worst-case of O(mn(m+n)) that can often be reduced to O(mn) through optimizations.
  • The use of non-affine gap penalties significantly enhances the probability of detecting sequence similarities containing long gaps.
  • The algorithm computes optimal local alignments for sequences of lengths m and n.

Conclusions:

  • The developed algorithm provides a more biologically accurate method for sequence alignment by employing non-linear gap penalties.
  • This approach improves the sensitivity of similarity detection, particularly for alignments involving extended insertions or deletions.
  • The algorithm offers an efficient computational solution for sequence alignment problems in bioinformatics.