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

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
RNA-seq03:21

RNA-seq

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 microarray-based...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...

You might also read

Related Articles

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

Sort by
Same author

Improved selection of canonical proteins for reference proteomes.

NAR genomics and bioinformatics·2024
Same author

Comparison of detection methods and genome quality when quantifying nuclear mitochondrial insertions in vertebrate genomes.

Frontiers in genetics·2022
Same author

Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction.

PloS one·2019
Same author

Risk-based Monitoring of Clinical Trials: An Integrative Approach.

Clinical therapeutics·2018
Same author

Using SQL Databases for Sequence Similarity Searching and Analysis.

Current protocols in bioinformatics·2017
Same author

Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold.

Nucleic acids research·2016

Related Experiment Video

Updated: Jul 5, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Using relational databases for improved sequence similarity searching and large-scale genomic analyses.

Aaron J Mackey1, William R Pearson

  • 1University of Virginia, Charlottesville, Virginia, USA.

Current Protocols in Bioinformatics
|April 23, 2008
PubMed
Summary

Relational databases streamline large-scale genomic analyses by efficiently managing sequence data and improving similarity searches. This approach enhances the statistical significance and analytical power for comparative genomics.

More Related Videos

Databases to Efficiently Manage Medium Sized, Low Velocity, Multidimensional Data in Tissue Engineering
09:43

Databases to Efficiently Manage Medium Sized, Low Velocity, Multidimensional Data in Tissue Engineering

Published on: November 22, 2019

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
09:14

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

Related Experiment Videos

Last Updated: Jul 5, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Databases to Efficiently Manage Medium Sized, Low Velocity, Multidimensional Data in Tissue Engineering
09:43

Databases to Efficiently Manage Medium Sized, Low Velocity, Multidimensional Data in Tissue Engineering

Published on: November 22, 2019

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
09:14

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Relational databases are crucial for managing and analyzing large datasets in genomics.
  • Efficiently handling sequence data is vital for large-scale genomic studies and homology detection.

Purpose of the Study:

  • To demonstrate the use of relational databases for enhancing sequence similarity searching.
  • To illustrate large-scale genomic analyses using homology-related data.
  • To provide protocols for installing and utilizing a protein sequence database (seqdb_demo).

Main Methods:

  • Installation and basic usage of the seqdb_demo protein sequence database.
  • Generating sequence library subsets for focused similarity searches.
  • Extending seqdb_demo for storing and analyzing sequence similarity search results.

Main Results:

  • Improved efficiency in sequence similarity searching through database subsetting.
  • Successful storage and retrieval of sequence similarity search results.
  • Application of stored search results for comparative genomic analysis.

Conclusions:

  • Relational databases significantly simplify and enhance large-scale genomic analyses.
  • Database-driven approaches improve the statistical power and scope of homology searches.
  • The seqdb_demo provides a practical framework for genomic data management and analysis.