Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Causes of Similarity-Dissimilarity Effect

Causes of Similarity-Dissimilarity Effect

The similarity-dissimilarity effect, a fundamental concept in social psychology, explains how interpersonal similarities and differences influence attraction and social interactions. This effect is supported by three key psychological perspectives: balance theory, social comparison theory, and consensual validation.Balance Theory and Cognitive ConsistencyBalance theory, developed by Fritz Heider, posits that individuals seek cognitive consistency in their relationships. When two people share...

Factors Influencing Attraction III: Similarity

Factors Influencing Attraction III: Similarity

The similarity hypothesis suggests that individuals are more likely to form relationships with others who share similar attitudes, beliefs, values, and interests. This concept has been widely studied in social psychology, demonstrating that perceived similarity fosters interpersonal attraction. In an experiment supporting this hypothesis, participants were presented with fabricated information indicating that strangers held attitudes similar to their own. The results showed that participants...

Cis-regulatory Sequences

Cis-regulatory Sequences

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...

Sequences

Sequences

Sequences are fundamental mathematical objects consisting of ordered lists of numbers that follow a specific rule or pattern. Sequences are critical in various mathematical concepts, including calculus, series, and number theory. They can model real-world phenomena such as population growth, financial investments, and physical processes like the diminishing height of a bouncing ball.Each number in a sequence is referred to as a term. Typically, the terms are denoted as a1, a2, a3,…, where...

Sanger Sequencing

Sanger Sequencing

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...

Arithmetic Sequences

Arithmetic Sequences

An arithmetic sequence is a structured arrangement of numbers where each term is derived by adding a constant value, known as the common difference, to the previous term. This consistent pattern allows for the efficient computation of any term within the sequence as well as the cumulative sum of multiple terms. The formula for finding the nth term of an arithmetic sequence is:Here, aₙ represents the nth term of the sequence, a is the first term, d is the common difference, and n is the...

You might also read

Related Articles

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

Sort by

Same author

Are Children Like Werewolves? Full Moon and Its Association with Sleep and Activity Behaviors in an International Sample of Children.

Frontiers in pediatrics·2016

Same author

MAP30 inhibits autophagy through enhancing acetyltransferase p300 and induces apoptosis in acute myeloid leukemia cells.

Oncology reports·2016

Same author

Fluoxetine protects against IL-1β-induced neuronal apoptosis via downregulation of p53.

Neuropharmacology·2016

Same author

Physical activity, sedentary behaviors and risk of gestational diabetes mellitus: a population-based cross-sectional study in Tianjin, China.

European journal of endocrinology·2016

Same author

Building Structured Personal Health Records from Photographs of Printed Medical Records.

AMIA ... Annual Symposium proceedings. AMIA Symposium·2016

Same author

AEG-1/MTDH-activated autophagy enhances human malignant glioma susceptibility to TGF-β1-triggered epithelial-mesenchymal transition.

Oncotarget·2016

Same journal

De Novo Protein Design Using the Blueprint Builder in Rosetta.

Current protocols in protein science·2020

Same journal

Methods for Expression of Recombinant Proteins Using a Pichia pastoris Cell-Free System.

Current protocols in protein science·2020

Same journal

Histone Purification Combined with High-Resolution Mass Spectrometry to Examine Histone Post-Translational Modifications and Histone Variants in Caenorhabditis elegans.

Current protocols in protein science·2020

Same journal

A Rapid and Facile Purification Method for Glycan-Binding Proteins and Glycoproteins.

Current protocols in protein science·2020

Same journal

Synthesis of Recombinant Human Hemoglobin With NH<sub>2</sub> -Terminal Acetylation in Escherichia coli.

Current protocols in protein science·2020

Same journal

A Fluorescence-Based Assay to Monitor SUMOylation in Real-Time.

Current protocols in protein science·2020

See all related articles

Search research articles

Related Experiment Video

Updated: Feb 6, 2026

Pattern-based Search of Epigenomic Data Using GeNemo

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

Sequence Similarity Searching.

Gang Hu¹, Lukasz Kurgan²

¹School of Mathematical Sciences and LPMC, Nankai University, Tianjin, China.

Current Protocols in Protein Science

|August 14, 2018

Summary

This summary is machine-generated.

Sequence similarity searching is crucial for analyzing biological data. This guide covers BLAST tools for sequence alignment, database searching, and recent advancements like MMseqs2.

Keywords:

BLAST BLASTN BLASTP MMseqs2 PSSM alignment sequence similarity searching

More Related Videos

Author Spotlight: Exploring Behavioral Pathways Through Cross-Species Insights in Foraging and Communication

Author Spotlight: Exploring Behavioral Pathways Through Cross-Species Insights in Foraging and Communication

Published on: November 17, 2023

A Psychophysics Paradigm for the Collection and Analysis of Similarity Judgments

A Psychophysics Paradigm for the Collection and Analysis of Similarity Judgments

Published on: March 1, 2022

Related Experiment Videos

Last Updated: Feb 6, 2026

Pattern-based Search of Epigenomic Data Using GeNemo

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

Author Spotlight: Exploring Behavioral Pathways Through Cross-Species Insights in Foraging and Communication

Author Spotlight: Exploring Behavioral Pathways Through Cross-Species Insights in Foraging and Communication

Published on: November 17, 2023

A Psychophysics Paradigm for the Collection and Analysis of Similarity Judgments

A Psychophysics Paradigm for the Collection and Analysis of Similarity Judgments

Published on: March 1, 2022

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Sequence similarity searching is integral to molecular biology, aiding in the analysis of vast sequence datasets.
It is used to infer function, structure, and evolutionary relationships from unannotated sequences.

Purpose of the Study:

To introduce and explain the widely-used BLAST family of sequence similarity search tools.
To guide users on performing sequence similarity searches using web-based and standalone BLAST+ tools.
To highlight recent advancements in the field, including the MMseqs2 method.

Main Methods:

Explanation of core concepts in sequence alignment.
Demonstration of database searching using BLASTP, PSI-BLAST, and BLASTN web interfaces.
Description of the standalone BLAST+ software, including input, parameters, and output.

Main Results:

Comprehensive overview of BLAST tool functionalities for sequence similarity searching.
Practical guidance on utilizing various BLAST versions for biological data analysis.
Introduction to MMseqs2 as a fast alternative for sequence similarity searching.

Conclusions:

BLAST tools are essential for modern molecular biology research.
Understanding BLAST parameters and outputs is key for accurate sequence analysis.
Emerging tools like MMseqs2 offer enhanced speed and efficiency for large-scale sequence comparisons.