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

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...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Sanger Sequencing01:57

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...
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...
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...

You might also read

Related Articles

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

Sort by
Same author

Double-negative (CD27<sup>-</sup>IgD<sup>-</sup>) B cells are expanded in NSCLC and inversely correlate with affinity-matured B cell populations.

Journal of translational medicine·2018
Same author

Using logistic regression to improve the prognostic value of microarray gene expression data sets: application to early-stage squamous cell carcinoma of the lung and triple negative breast carcinoma.

BMC medical genomics·2014
Same author

Alisertib added to rituximab and vincristine is synthetic lethal and potentially curative in mice with aggressive DLBCL co-overexpressing MYC and BCL2.

PloS one·2014
Same author

In Vitro Assessment of the Inflammatory Breast Cancer Cell Line SUM 149: Discovery of 2 Single Nucleotide Polymorphisms in the RNase L Gene.

Journal of Cancer·2013
Same author

Choosing a method for phylogenetic prediction.

CSH protocols·2011
Same author

Maximum parsimony method for phylogenetic prediction.

CSH protocols·2011
Same journal

Emerging Trends in Mass Spectrometry-Based Quantitative Proteome and Phosphoproteome Profiling in Maize.

Cold Spring Harbor protocols·2026
Same journal

Sample Preparation for Quantitative Proteome and Phosphoproteome Profiling of Maize Tissues.

Cold Spring Harbor protocols·2026
Same journal

High-Throughput Microbial Assay for Amino Acid Measurement in Ground Maize Seed Samples Utilizing Auxotrophic <i>E. coli</i>.

Cold Spring Harbor protocols·2025
Same journal

Grain Quality in Maize.

Cold Spring Harbor protocols·2025
Same journal

High-Throughput Assay for Measuring Phytate and Available Phosphorus in Ground Maize Seed Samples.

Cold Spring Harbor protocols·2025
Same journal

Functional Genomic Analysis of Transposon Insertion Mutant Maize Plants from the UniformMu National Public Resource.

Cold Spring Harbor protocols·2025
See all related articles

Related Experiment Video

Updated: Jun 16, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Using multiple sequence alignment editors and formatters.

David W Mount

    Cold Spring Harbor Protocols
    |February 12, 2010
    PubMed
    Summary
    This summary is machine-generated.

    Sequence alignment editors and formatters help researchers manually refine multiple sequence alignments (MSAs) for better biological insights. These tools support various input/output formats and enhance visualization for improved analysis.

    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

    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

    Related Experiment Videos

    Last Updated: Jun 16, 2026

    A Practical Guide to Phylogenetics for Nonexperts
    12:00

    A Practical Guide to Phylogenetics for Nonexperts

    Published on: February 5, 2014

    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

    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

    Area of Science:

    • Bioinformatics
    • Computational Biology
    • Genomics

    Background:

    • Manual editing of multiple sequence alignments (MSAs) is crucial for refining biological interpretations.
    • Existing tools often lack flexibility in handling diverse sequence formats and output options.

    Purpose of the Study:

    • To introduce and review sequence alignment editors and formatters.
    • To provide resources for researchers needing to manipulate and visualize MSAs.

    Main Methods:

    • Description of functionalities of sequence alignment editors for manual sequence manipulation.
    • Overview of sequence formatters for customizing MSA visualization and output.

    Main Results:

    • Editors allow sequence reordering and modification using standard computer commands.
    • Formatters support various output formats (e.g., Postscript, RTF) and input formats (e.g., MSF, FASTA).

    Conclusions:

    • Sequence alignment editors and formatters are valuable tools for bioinformatics research.
    • These tools enhance the accuracy and presentation of multiple sequence alignments.