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

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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 form...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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 form...
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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 DNA...

You might also read

Related Articles

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

Sort by
Same author

Large-scale land acquisitions exacerbate local farmland inequalities in Tanzania.

Proceedings of the National Academy of Sciences of the United States of America·2023
Same author

Carbon emissions from the global land rush and potential mitigation.

Nature food·2023
Same author

Computational Creativity and Aesthetics with Algorithmic Information Theory.

Entropy (Basel, Switzerland)·2021
Same author

On the Problem of Small Objects.

Entropy (Basel, Switzerland)·2021
Same author

Mean and Variance of Phylogenetic Trees.

Systematic biology·2019
Same author

Estimating local biodiversity change: a critique of papers claiming no net loss of local diversity.

Ecology·2016

Related Experiment Video

Updated: Jul 19, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Optimizing multiple seeds for protein homology search.

Daniel G Brown1

  • 1School of Computer Science, University of Waterloo, 200 University Ave., West, Waterloo, ON N2L 3G1, Canada. browndg@uwaterloo.ca

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|October 19, 2006
PubMed
Summary

This study introduces a new framework using vector seeds to improve local protein alignment algorithms, significantly reducing false positives while maintaining high sensitivity.

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

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

Related Experiment Videos

Last Updated: Jul 19, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

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

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

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Local protein alignment is crucial for understanding protein function and evolution.
  • Existing algorithms like BLASTP can generate noise hits, impacting accuracy.
  • Improving the efficiency and accuracy of protein alignment is an ongoing challenge.

Purpose of the Study:

  • To develop a novel framework for enhancing local protein alignment algorithms.
  • To reduce false positive hits in protein sequence comparisons.
  • To maintain or improve the sensitivity of alignment methods.

Main Methods:

  • Extending local protein aligners with a collection of vector or ungapped alignment seeds.
  • Modeling the selection of seed models as an integer programming problem.
  • Developing algorithms to efficiently choose optimal seed sets.

Main Results:

  • The proposed method significantly reduces noise hits.
  • Achieved a four to five times reduction in false positive hits.
  • Preserved essentially identical sensitivity compared to BLASTP.

Conclusions:

  • The framework effectively improves local protein alignment.
  • Vector seeds offer a practical solution for reducing false positives in sequence alignment.
  • This approach enhances the reliability of protein similarity searches.