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

Next-generation Sequencing03:00

Next-generation Sequencing

87.4K
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....
87.4K
Sanger Sequencing01:57

Sanger Sequencing

752.8K
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...
752.8K
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

11.1K
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...
11.1K
Gene Conversion02:08

Gene Conversion

9.7K
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
9.7K
RNA-seq03:21

RNA-seq

9.8K
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...
9.8K
DNA Base Pairing02:27

DNA Base Pairing

26.9K
Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,
26.9K

You might also read

Related Articles

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

Sort by
Same author

Deciphering tRNA repertoires and translation coordination during mouse early embryogenesis by ORACLE-tRNAseq.

Nature communications·2026
Same author

Epitranscriptomic regulation of mRNA stability in pivotal transcription factors modulates the second cell fate decision.

Nature communications·2026
Same author

Weaning drives microbiome-mediated epigenetic regulation to shape immune memory in mice.

Nature microbiology·2026
Same author

Endogenous retroviruses synthesize heterologous chimeric RNAs to reinforce human early embryo development.

Science (New York, N.Y.)·2026
Same author

Systematic evaluation of computational tools for multitype RNA modification detection using nanopore direct RNA sequencing.

Nature methods·2025
Same author

Epigenetic regulation of ACSL4 via H2A monoubiquitylation connects lipid metabolism to BAP1-mediated ferroptosis.

Cell death and differentiation·2025

Related Experiment Video

Updated: Jun 5, 2025

Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

37.0K

BASAL: a universal mapping algorithm for nucleotide base-conversion sequencing.

Moping Xu1,2, Xiaoyang Liu3, Miao Wang1,2

  • 1Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, 389 Xincun Road, Shanghai 200065, China.

Nucleic Acids Research
|December 10, 2024
PubMed
Summary
This summary is machine-generated.

BASAL (BAse-conversion Sequencing ALigner) accurately maps diverse RNA and DNA base modifications. This new tool enhances epigenomic and epitranscriptomic research by improving analysis accuracy and efficiency.

More Related Videos

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.0K
Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

25.5K

Related Experiment Videos

Last Updated: Jun 5, 2025

Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

37.0K
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

12.0K
Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

25.5K

Area of Science:

  • Epigenetics
  • Molecular Biology
  • Bioinformatics

Background:

  • Base-conversion (BC) techniques enable single-base resolution profiling of RNA and DNA modifications.
  • Diverse BC strategies, including one-way, multi-way, and deletion-induced conversions, present challenges for existing sequence aligners.
  • Current aligners often exhibit misalignments and inefficiencies when processing BC data.

Purpose of the Study:

  • To introduce BASAL (BAse-conversion Sequencing ALigner), a novel sequence aligner designed to handle diverse BC strategies.
  • To improve the accuracy and efficiency of mapping RNA and DNA modification sequencing data.
  • To facilitate advanced epigenomic and epitranscriptomic analyses, including single-cell studies.

Main Methods:

  • Development of BASAL utilizing bit-masking technology for accurate mismatch penalty calculation.
  • Implementation of support for a comprehensive range of BC strategies.
  • Validation using simulated and real sequencing data, alongside experimental verification.

Main Results:

  • BASAL demonstrates superior mapping accuracy and efficiency compared to state-of-the-art tools.
  • The aligner effectively identifies reliable RNA and DNA modification sites.
  • BASAL enhances single-cell m6A analysis, revealing cell subpopulations and evolutionary trajectories.

Conclusions:

  • BASAL is a versatile and accurate universal aligner for RNA and DNA modification sequencing.
  • The tool overcomes limitations of existing aligners in handling diverse BC strategies.
  • BASAL is poised to drive significant advancements in epigenomics and epitranscriptomics research.