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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.

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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...

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Updated: Jul 1, 2025

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

CNCA aligns small annotated genomes.

Jean-Noël Lorenzi^1,2,3, François Graner^4,5, Virginie Courtier-Orgogozo^4,6

¹Université Paris Cité, Paris, France. jean-noel.lorenzi@ijm.fr.

BMC Bioinformatics

|February 29, 2024

Summary

This summary is machine-generated.

A new web tool, CNCA (Conserved Non-coding Sequence Aligner), aligns small genomes, including non-coding DNA, crucial for evolutionary studies like SARS-CoV-2 origins.

Keywords:

Annotated genomes Nucleotide alignment Protein alignment

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Area of Science:

Genomics
Bioinformatics
Evolutionary Biology

Background:

Accurate sequence alignment is essential for evolutionary studies.
Aligning closely related genomes, including non-coding regions, is challenging.
Existing tools do not adequately address the alignment of small, conserved genomes.

Purpose of the Study:

To develop a novel tool for aligning small, closely related genomes.
To integrate both coding and non-coding sequences into a single alignment.
To facilitate evolutionary analyses, particularly for viral genomes like SARS-CoV-2.

Main Methods:

CNCA is a web-based tool accepting GenBank files.
It performs an initial nucleotide alignment, refined by protein sequence alignment.
Ensures nucleotide-protein alignment consistency and prevents frameshifts.

Main Results:

CNCA generates accurate multiple nucleotide alignments of small genomes (up to 50 kb).
The alignment integrates both coding and non-coding sequences.
The tool guarantees frameshift-free alignments that match protein sequence alignments.

Conclusions:

CNCA enables comprehensive genome alignment by including non-coding regions.
This method preserves evolutionary information often lost in traditional approaches.
CNCA is valuable for studying the evolution of small genomes, including viruses.