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

RNA-seq

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...

Multi-species Conserved Sequences

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...

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...

Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

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.

You might also read

Related Articles

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

Sort by

Same author

Filling the mechanistic and methodological gaps for predicting cytokine release syndrome in humans.

Frontiers in pharmacology·2026

Same author

Publisher Correction: Unsupervised risk factor identification across cancer types and data modalities via explainable artificial intelligence.

NPJ digital medicine·2026

Same author

Preclinical evaluation of a novel CD4 specific CAR NK cell therapy for T-cell malignancies.

Cytotherapy·2026

Same author

Unsupervised risk factor identification across cancer types and data modalities via explainable artificial intelligence.

NPJ digital medicine·2026

Same author

Body composition predicts poor outcomes and reveals immunometabolic dysfunction via single-cell profiling in anti-BCMA CAR T-treated myeloma.

HemaSphere·2026

Same author

A review and update of the distribution, bionomics, and medical importance of Culicoides (Haematomyidium) paraensis (Diptera: Ceratopogonidae) in the United States in response to recent Oropouche virus expansion in the Americas.

Journal of medical entomology·2026

Search research articles

Related Experiment Video

Updated: Jul 4, 2026

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences.

Dominic Rose¹, Jana Hertel, Kristin Reiche

¹Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.

|May 31, 2008

Summary

NcDNAlign generates high-quality multiple sequence alignments for non-coding DNA efficiently. This versatile pipeline accelerates comparative genomics, aiding in novel ncRNA discovery and identifying conserved noncoding DNA across species.

More Related Videos

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

Published on: June 20, 2018

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Related Experiment Videos

Last Updated: Jul 4, 2026

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

Published on: June 20, 2018

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Area of Science:

Comparative genomics
Bioinformatics
Computational biology

Background:

Genome-wide multiple sequence alignments (MSAs) are crucial for comparative genomics.
Existing methods can be computationally intensive, limiting their application in large-scale studies.

Purpose of the Study:

To present NcDNAlign, a versatile and efficient pipeline for generating high-quality MSAs of non-protein-coding sequences.
To demonstrate the utility of NcDNAlign in identifying novel non-coding RNAs and conserved noncoding DNA.

Main Methods:

NcDNAlign combines pairwise BLAST alignments for initial MSAs, followed by local improvement and trimming.
The pipeline is optimized for speed, making it suitable for pilot studies and large-scale genome analysis.

Main Results:

NcDNAlign significantly reduces CPU time (20-30 fold) compared to TBA for gammaproteobacterial alignments.
Case studies showed similar sensitivity and false discovery rates for ncRNA prediction and identification of ultra-conserved regions, yielding novel evolutionary insights.

Conclusions:

NcDNAlign provides an efficient and reliable solution for genome-wide alignment of non-coding sequences.
The pipeline facilitates the discovery of novel ncRNAs and conserved noncoding DNA, advancing comparative genomic research.