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

Wilcoxon Signed-Ranks Test for Matched Pairs01:09

Wilcoxon Signed-Ranks Test for Matched Pairs

197
The Wilcoxon signed-rank test for matched pairs evaluates the null hypothesis by combining the ranks of differences with their signs. It essentially tests whether the median of the differences in a population of matched pairs is zero. Since the test incorporates more information than the sign test, it generally yields more trustable conclusions. This test also does not require the data to follow a normal distribution, but two conditions must be met for it to be applicable: (1) the data must...
197
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.1K
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...
6.1K
¹H NMR: Long-Range Coupling01:27

¹H NMR: Long-Range Coupling

1.9K
The coupling interactions of nuclei across four or more bonds are usually weak, with J values less than 1 Hz. While these are usually not observed in spectra, the presence of multiple bonds along the coupling pathway can result in observable long-range coupling.
In alkenes, spin information is communicated via σ–π overlap, as seen in allylic (four-bond) and homoallylic (five-bond) couplings. These coupling interactions are stronger when the σ bond is parallel to the alkene...
1.9K
DNA Base Pairing02:27

DNA Base Pairing

27.9K
Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,
27.9K
Phylogenetic Trees03:21

Phylogenetic Trees

45.9K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
45.9K
Conserved Binding Sites01:49

Conserved Binding Sites

4.3K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.3K

You might also read

Related Articles

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

Sort by
Same author

Predicting and Comparing Students' Online and Offline Academic Performance Using Machine Learning Algorithms.

Behavioral sciences (Basel, Switzerland)·2023
Same author

An Elastic Self-Adjusting Technique for Rare-Class Synthetic Oversampling Based on Cluster Distortion Minimization in Data Stream.

Sensors (Basel, Switzerland)·2023
Same author

Similarity-Based Adaptive Window for Improving Classification of Epileptic Seizures with Imbalance EEG Data Stream.

Entropy (Basel, Switzerland)·2022
Same author

Membrane Clustering of Coronavirus Variants Using Document Similarity.

Genes·2022
Same author

A Novel Methodology for Measuring the Abstraction Capabilities of Image Recognition Algorithms.

Journal of imaging·2021

Related Experiment Video

Updated: Aug 22, 2025

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

7.4K

Heuristic Pairwise Alignment in Database Environments.

Panna Lipták1, Attila Kiss1,2, János Márk Szalai-Gindl1

  • 1Department of Information Systems, ELTE Eötvös Loránd University, 1117 Budapest, Hungary.

Genes
|November 11, 2022
PubMed
Summary
This summary is machine-generated.

Managing biological data, especially DNA sequences, is challenging. This study introduces a novel heuristic pairwise alignment method within a database, using MonetDB to accelerate sequence analysis.

Keywords:
bioinformaticsdatabase systemspairwise alignment

More Related Videos

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

7.1K
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.4K

Related Experiment Videos

Last Updated: Aug 22, 2025

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

7.4K
Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

7.1K
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.4K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Database Management

Background:

  • Biological data, particularly DNA sequences, are increasingly accessible but pose management and processing challenges.
  • Current bioinformatics workflows often perform sequence analysis outside of database systems, leading to inefficiencies.
  • Efficient management and analysis of large biological datasets are critical for scientific advancement.

Purpose of the Study:

  • To propose a novel approach for comparative sequence analysis using heuristic pairwise alignment.
  • To integrate sequence alignment algorithms directly within a database environment.
  • To leverage database management system benefits for accelerated sequence alignment.

Main Methods:

  • Development of a heuristic pairwise alignment method executed inside a database.
  • Utilizing a column-oriented database system, specifically MonetDB, for data storage and processing.
  • Exploiting data similarities within the database to optimize alignment algorithm performance.

Main Results:

  • Demonstration of a novel heuristic pairwise alignment approach within a database.
  • Successful integration of alignment algorithms into the database environment.
  • Identification of performance benefits through the use of MonetDB and heuristic methods.

Conclusions:

  • The proposed in-database heuristic alignment method offers an efficient solution for biological sequence analysis.
  • Column-oriented databases like MonetDB provide significant advantages for accelerating bioinformatics algorithms.
  • Integrating analysis directly within databases streamlines workflows and enhances the processing of large-scale biological data.