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

Genome Annotation and Assembly

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.

Evolutionary Relationships through Genome Comparisons

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...

You might also read

Related Articles

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

Sort by

Same author

Cumulative Antigen Suppression Reduces Clonal Plasma Cell Evolution in Gaucher Disease.

American journal of hematology·2026

Same author

MAGIC: Meta-Ability Guided Interactive Chain-of-Distillation for Effective-and-Efficient Vision-and-Language Navigation.

IEEE transactions on pattern analysis and machine intelligence·2026

Same author

A comprehensive discovery platform for ELOVL1 small-molecule inhibitors targeting very long-chain fatty acid synthesis in adrenoleukodystrophy.

The Journal of biological chemistry·2026

Same author

TMEM121 suppresses cervical cancer cell proliferation and migration via interaction with the ERK pathway.

American journal of cancer research·2026

Same author

AAV gene therapy for GBA1-related diseases.

Molecular therapy : the journal of the American Society of Gene Therapy·2025

Same author

Comparative outcomes of laparoscopic lateral suspension, sacrocolpopexy, and transvaginal mesh for advanced apical prolapse: A retrospective cohort study.

PloS one·2025

Search research articles

Related Experiment Video

Updated: Sep 9, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

Panaln: indexing pangenome for read alignment.

Lilu Guo¹, Zongtao He¹, Hongwei Huo¹

¹Department of Computer Science, Xidian University, Xi'an 710071, China.

Bioinformatics (Oxford, England)

|August 28, 2025

Summary

Panaln, a new wavelet tree-based pangenome index, offers a scalable and accurate solution for biological sequence analysis. It significantly reduces space requirements while improving read alignment accuracy compared to existing methods.

More Related Videos

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue

Published on: November 21, 2018

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

Published on: May 19, 2019

Related Experiment Videos

Last Updated: Sep 9, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue

Chromatin Immunoprecipitation of Murine Brown Adipose Tissue

Published on: November 21, 2018

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

Published on: May 19, 2019

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Pangenome indexing is crucial for biological sequence analysis, particularly for read alignment.
Accurate identification of sequencing fragments with errors and variants necessitates scalable pangenome indexing.

Purpose of the Study:

To introduce Panaln, a novel wavelet tree-based approach for pangenome indexing.
To develop efficient methods for count queries and read alignment using the Panaln index.

Main Methods:

Wavelet tree-based pangenome indexing (Panaln).
Batch computation for fast count queries.
Seeding strategy and seed-and-extend paradigm for read alignment.
Linear model representation for scalable index construction.

Main Results:

Panaln demonstrates significantly reduced space usage compared to other pangenome methods.
Achieves generally higher accuracy in read alignment.
Provides enhanced accuracy over popular single-reference methods.
Scalable index construction is achieved through a linear model representation.

Conclusions:

Panaln offers a space-efficient and accurate solution for pangenome indexing.
The approach improves read alignment performance, especially in the presence of sequencing errors and genomic variants.
Panaln represents a significant advancement in scalable pangenome indexing for biological sequence analysis.