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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.

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...

Next-generation Sequencing

Next-generation Sequencing

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.

Sanger Sequencing

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...

RACE - Rapid Amplification of cDNA Ends

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...

Maxam-Gilbert Sequencing

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...

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Related Experiment Video

Updated: Jun 26, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Sequence assembly.

K Scheibye-Alsing¹, S Hoffmann, A Frankel

¹Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.

Computational Biology and Chemistry

|January 21, 2009

Summary

This summary is machine-generated.

This study reviews computational assembly programs for large-scale sequencing data, highlighting unresolved issues and key concerns like repetitive DNA sequences. It offers a guide to available tools for genome projects.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Genome sequencing is rapidly advancing, generating vast amounts of data.
Computational assembly is essential for processing this large-scale sequencing data in genome projects.
Existing challenges in computational assembly remain unresolved, impacting data interpretation.

Purpose of the Study:

To provide a comprehensive overview of currently available public sequence assembly programs.
To describe the fundamental principles and challenges of computational assembly.
To offer resources for selecting and downloading assembly tools.

Main Methods:

Literature review of existing sequence assembly programs.
Analysis of core principles in computational genome assembly.
Summary and comparison of different assembly algorithms.
Compilation of download and usage information for selected tools.

Main Results:

Identification of key challenges in computational assembly, including repetitive sequences and alternative transcripts.
Overview of various publicly available sequence assembly programs.
Summary of existing comparative studies on different assemblers.
A curated list of assembly programs with download directions provided.

Conclusions:

Computational assembly remains a critical yet challenging aspect of large-scale genomics.
A comprehensive understanding of assembly principles and available tools is crucial for researchers.
The provided resource aims to aid researchers in selecting appropriate assembly programs for their genome projects.