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

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

8.8K
Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
8.8K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.9K
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...
4.9K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

15.0K
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...
15.0K
Nucleic Acid Structure01:25

Nucleic Acid Structure

10.1K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
10.1K
Conservation of Protein Domains02:26

Conservation of Protein Domains

4.3K
4.3K
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

2.9K
Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called...
2.9K

You might also read

Related Articles

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

Sort by
Same author

Method for identification of 10 SSR markers from monkey genomes and its statistical inference with One & Two-way ANOVA.

MethodsX·2022
Same author

Data of 10 SSR markers for genomes of homo sapiens and monkeys.

Data in brief·2017
Same author

Similarity analysis between chromosomes of Homo sapiens and monkeys with correlation coefficient, rank correlation coefficient and cosine similarity measures.

Genomics data·2016
See all related articles

Related Experiment Video

Updated: Mar 24, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

70.1K

Next generation sequencing (NGS) database for tandem repeats with multiple pattern 2°-shaft multicore string

Chinta Someswara Rao1, S Viswanadha Raju2

  • 1Department of CSE, SRKR Engineering College, Bhimavaram, AP, India.

Genomics Data
|March 17, 2016
PubMed
Summary

This study introduces TandemRepeatDB, a new resource for analyzing simple sequence repeats (SSRs) across multiple primate genomes using next-generation sequencing (NGS) data. It details SSR frequencies for 10 specific motifs in various species.

Keywords:
GenomeNGSSSRString matchingTandemRepeatDBchromosomes

More Related Videos

The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

32.5K
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

1.3K

Related Experiment Videos

Last Updated: Mar 24, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

70.1K
The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

32.5K
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

1.3K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Next-generation sequencing (NGS) has become a pivotal technology in biomedical and biological research.
  • Comprehensive resources are needed to analyze the vast amounts of genomic data generated by NGS.

Purpose of the Study:

  • To develop a comprehensive resource for analyzing tandem repeats in primate genomes.
  • To provide a database of simple sequence repeat (SSR) frequencies for multiple species.

Main Methods:

  • Considered 10 specific tandem repeat loci (TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG, TCTA).
  • Developed the NGS Tandem Repeat Database (TandemRepeatDB) for Homo sapiens and nine other primate species.
  • Analyzed SSR occurrence frequency on a chromosome-by-chromosome basis using multicore string matching.

Main Results:

  • Successfully cataloged SSR frequencies for 10 motifs across multiple primate genomes.
  • The TandemRepeatDB provides a detailed resource for SSR distribution in the studied species.
  • Identified variations in SSR occurrence across different chromosomes and species.

Conclusions:

  • TandemRepeatDB serves as a valuable resource for researchers utilizing NGS data in comparative genomics and evolutionary studies.
  • The findings highlight the utility of computational approaches for analyzing repetitive elements in complex genomes.
  • This database facilitates further research into the functional roles and evolutionary dynamics of SSRs in primates.