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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.

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.

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...

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Related Experiment Video

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Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Next generation transcriptomes for next generation genomes using est2assembly.

Alexie Papanicolaou¹, Remo Stierli, Richard H Ffrench-Constant

¹Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany. alexie@butterflybase.org

BMC Bioinformatics

|December 26, 2009

Summary

Researchers can now analyze transcriptome data from non-model species using the semi-automated est2assembly platform. This tool processes Sanger and 454 sequencing data for efficient hybrid de novo assembly and annotation.

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Area of Science:

Bioinformatics
Genomics
Transcriptomics

Background:

Decreasing costs of sequencing technologies (Sanger, 454 pyrosequencing) enable extensive transcriptome projects in non-model species.
Rapid data generation outpaces analytical capabilities for researchers studying non-model organisms.

Purpose of the Study:

To present est2assembly, a semi-automated platform for processing and assembling transcriptome data.
To facilitate the analysis and annotation of sequence data from non-model species.

Main Methods:

Development of a semi-automated platform, est2assembly.
Processing of raw sequence data from Sanger and 454 platforms.
Hybrid de novo assembly and annotation of transcriptome data.
Generation of GMOD compatible output and SeqFeature databases for GBrowse.

Main Results:

est2assembly successfully processed public Sanger EST data (Drosophila, Bicyclus) and new insect transcriptome collections.
Comparison with published 454 data validated the platform's performance.
Users can parameterize assembler variables and assess assembly quality for optimal results.

Conclusions:

Assembler parameterization and standardized quality assessment are crucial for EST projects.
Shallow 454 sequencing provides sufficient data for broad community use.
est2assembly aids manual curation of gene models, particularly for species targeted for future genome projects using Next Generation Sequencing.