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

Global Climate Change01:50

Global Climate Change

29.0K
Throughout its ~4.5 billion year history, the Earth has experienced periods of warming and cooling. However, the current drastic increase in global temperatures is well outside of the Earth’s cyclic norms, and evidence for human-caused global climate change is compelling. Paleoclimatology, the study of ancient climate conditions, provides ample evidence for human-caused global climate change by comparing recent conditions with those in the past.
29.0K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

11.9K
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...
11.9K
From DNA to Protein03:06

From DNA to Protein

22.6K
The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
22.6K
Velocity of an Object01:18

Velocity of an Object

208
Understanding how an object moves along a path requires distinguishing between motion over a time span and motion at a precise moment. A useful example is a vehicle traveling along a straight and level path, where its position at any given time is known. The initial step in analyzing this motion is to measure how far the vehicle travels over a fixed time period. This measurement, called average velocity, is computed by dividing the total change in position by the duration over which the change...
208
DNA-only Transposons02:57

DNA-only Transposons

17.5K
DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
17.5K
Recombinant DNA01:09

Recombinant DNA

103.5K
Overview
103.5K

You might also read

Related Articles

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

Sort by
Same author

Percolation Images: Fractal Geometry Features for Brain Tumor Classification.

Advances in neurobiology·2024
Same author

OralEpitheliumDB: A Dataset for Oral Epithelial Dysplasia Image Segmentation and Classification.

Journal of imaging informatics in medicine·2024
Same author

Metaheuristics for multiple sequence alignment: A systematic review.

Computational biology and chemistry·2021
Same author

Unsupervised method for normalization of hematoxylin-eosin stain in histological images.

Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society·2019
Same author

Color normalization of faded H&E-stained histological images using spectral matching.

Computers in biology and medicine·2019
Same author

Hierarchical assessment of host factors influencing the spontaneous resolution of hepatitis C infection.

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]·2019

Related Experiment Video

Updated: Feb 10, 2026

Methodology to Test Control Agents and Insecticides Against the Coffee Berry Borer Hypothenemus hampei
09:23

Methodology to Test Control Agents and Insecticides Against the Coffee Berry Borer Hypothenemus hampei

Published on: March 23, 2022

2.4K

An approach for COFFEE objective function to global DNA multiple sequence alignment.

Anderson Rici Amorim1, Leandro Alves Neves1, Carlos Roberto Valêncio1

  • 1Department of Computer Science and Statistics, São Paulo State University, Rua Cristovão Colombo 2265, São José do Rio Preto, São Paulo, Brazil.

Computational Biology and Chemistry
|May 9, 2018
PubMed
Summary

This study modified the COFFEE objective function for the MSA-GA tool, improving multiple sequence alignment (MSA) for nucleotide sequences. The enhanced method shows superior and more reliable results compared to standard COFFEE and other tools.

Keywords:
Genetic AlgorithmMultiple sequence alignmentOptimization

More Related Videos

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

9.2K
The Hawaii Protocol for Scientific Monitoring of Coffee Berry Borer: a Model for Coffee Agroecosystems Worldwide
14:29

The Hawaii Protocol for Scientific Monitoring of Coffee Berry Borer: a Model for Coffee Agroecosystems Worldwide

Published on: March 19, 2018

8.5K

Related Experiment Videos

Last Updated: Feb 10, 2026

Methodology to Test Control Agents and Insecticides Against the Coffee Berry Borer Hypothenemus hampei
09:23

Methodology to Test Control Agents and Insecticides Against the Coffee Berry Borer Hypothenemus hampei

Published on: March 23, 2022

2.4K
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

9.2K
The Hawaii Protocol for Scientific Monitoring of Coffee Berry Borer: a Model for Coffee Agroecosystems Worldwide
14:29

The Hawaii Protocol for Scientific Monitoring of Coffee Berry Borer: a Model for Coffee Agroecosystems Worldwide

Published on: March 19, 2018

8.5K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment (MSA) is crucial for protein structure/function prediction and phylogenetic analysis.
  • Existing MSA tools like MSA-GA utilize genetic algorithms but have limitations with nucleotide sequences.
  • The COFFEE objective function, while effective for proteins, is not optimized for nucleotide MSA.

Purpose of the Study:

  • To modify the COFFEE objective function for improved multiple sequence alignment of nucleotide sequences.
  • To enhance the MSA-GA tool's capability to handle both protein and nucleotide sequence alignments effectively.
  • To assess the performance of the modified COFFEE function against existing methods.

Main Methods:

  • Modification of the COFFEE objective function to accommodate nucleotide sequence characteristics.
  • Integration of the modified COFFEE function into the MSA-GA tool.
  • Evaluation of the enhanced MSA-GA using benchmark datasets (BAliBase and BRAliBase) for nucleotide and protein alignments.

Main Results:

  • The modified COFFEE objective function achieved superior alignment results for nucleotide sequences compared to the standard COFFEE.
  • The enhanced MSA-GA demonstrated competitive or better performance against WSP for nucleotide sequence alignment across test cases.
  • The modified approach yielded more reliable results with reduced standard deviation variations.

Conclusions:

  • The modified COFFEE objective function significantly improves MSA for nucleotide sequences within the MSA-GA framework.
  • This enhancement broadens the applicability of MSA-GA to a wider range of biological sequence data.
  • The study provides a more robust and reliable tool for bioinformatics sequence analysis.