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

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.4K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.4K
Improving Translational Accuracy02:07

Improving Translational Accuracy

12.1K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
12.1K
Improving Translational Accuracy02:07

Improving Translational Accuracy

3.1K
3.1K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

13.4K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
13.4K
RNA-seq03:21

RNA-seq

10.8K
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...
10.8K
Sanger Sequencing01:57

Sanger Sequencing

763.4K
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...
763.4K

You might also read

Related Articles

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

Sort by
Same author

Targeting of the CD80/86 proinflammatory axis as a therapeutic strategy to prevent severe COVID-19.

Scientific reports·2021
Same author

Interactions between rheumatoid arthritis antibodies are associated with the response to anti-tumor necrosis factor therapy.

BMC musculoskeletal disorders·2021
Same author

Incidence of COVID-19 in a cohort of adult and paediatric patients with rheumatic diseases treated with targeted biologic and synthetic disease-modifying anti-rheumatic drugs.

Seminars in arthritis and rheumatism·2020
Same author

Scalable Consistency in T-Coffee Through Apache Spark and Cassandra Database.

Journal of computational biology : a journal of computational molecular cell biology·2018
Same author

A user-friendly web portal for T-Coffee on supercomputers.

BMC bioinformatics·2011
Same author

Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud.

Bioinformatics (Oxford, England)·2010
Same journal

Facial iPPG heatmap patterns based on period-aware autoencoder show association with carotid atherosclerosis towards non-contact hemodynamic assessment.

Computer methods and programs in biomedicine·2026
Same journal

Explainable machine learning models predict liver fibrosis risk and outcome in the general population: Development and multi-cohort external validation.

Computer methods and programs in biomedicine·2026
Same journal

Evaluation of surrogate endpoints for survival outcomes using the surrogate package in R.

Computer methods and programs in biomedicine·2026
Same journal

Relative spectral and frication-based descriptors as numerical indicators of place of articulation shifts in fricatives produced by Polish children.

Computer methods and programs in biomedicine·2026
Same journal

Leaflet resection improves valve expansion and hemodynamic performance in redo TAVI with balloon- and self-expanding transcatheter heart valve configurations.

Computer methods and programs in biomedicine·2026
Same journal

Spectral super-resolution for Parkinson's voice via representation-level methods under mixed-reality acquisition.

Computer methods and programs in biomedicine·2026
See all related articles

Related Experiment Video

Updated: Oct 31, 2025

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

2.9K

Accurate consistency-based MSA reducing the memory footprint.

Jordi Lladós1, Fernando Cores1, Fernando Guirado1

  • 1INSPIRES Research Center, Universitat de Lleida. Jaume II. 69, 25001 Lleida, Spain.

Computer Methods and Programs in Biomedicine
|July 1, 2021
PubMed
Summary
This summary is machine-generated.

Matrix-Based T-Coffee enhances multiple sequence alignment accuracy and scalability using library reductions and a complementary objective function. This method reduces memory footprint and execution time, improving performance for large datasets.

Keywords:
ConsistencyDynamic programmingMultiple sequence alignmentT-coffee

More Related Videos

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.6K
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

7.2K

Related Experiment Videos

Last Updated: Oct 31, 2025

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

2.9K
An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.6K
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

7.2K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Next-Generation Sequencing (NGS) drives demand for faster, more accurate multiple sequence alignment (MSA) tools.
  • Increasing sequence numbers and lengths challenge current MSA tools, demanding more system resources and reducing accuracy.
  • Consistency-based MSA methods exhibit high CPU and memory requirements, limiting scalability.

Purpose of the Study:

  • To enhance the scalability and performance of consistency-based MSA tools through library reductions.
  • To mitigate accuracy loss associated with extreme library reductions in MSA.
  • To introduce Matrix-Based T-Coffee, a novel consistency-based method addressing resource limitations.

Main Methods:

  • Developed Matrix-Based T-Coffee, a consistency-based method incorporating library reductions.
  • Utilized a complementary objective function to counteract accuracy degradation from library reduction.
  • Implemented the method within the T-Coffee framework to manage low memory resources.

Main Results:

  • Library reduction of ≥30% with a complementary objective function improved T-Coffee accuracy.
  • Library reduction of ≥50% resulted in reduced execution times and enhanced scalability.
  • The proposed method demonstrated improved performance under memory constraints.

Conclusions:

  • Matrix-Based T-Coffee achieves accurate alignments with improved scalability.
  • The method effectively reduces memory footprint and execution time.
  • These enhancements are potentially applicable to other consistency-based alignment tools.