ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes

Alessandro M Varani,Mick Chandler,Patricia Siguier,Edith Gourbeyre,Vincent Charneau

doi:10.1186/gb-2011-12-3-r30

Abstract

Insertion sequences (ISs) play a key role in prokaryotic genome evolution but are seldom well annotated. We describe a web application pipeline, ISsaga (http://issaga.biotoul.fr/ISsaga/issaga_index.php), that provides computational tools and methods for high-quality IS annotation. It uses established ISfinder annotation standards and permits rapid processing of single or multiple prokaryote genomes. ISsaga provides general prediction and annotation tools, information on genome context of individual ISs and a graphical overview of IS distribution around the genome of interest.

Highlights

The growing number of completely sequenced bacterial and archaeal genomes are making important contributions to understanding genome structure and evolution
High quality genome annotation together with a standardized nomenclature is an essential requirement for this since most proteins identified from these sequencing projects will probably never be characterized biochemically [1]
To overcome the present annotation limitations, we have developed ISsaga (Insertion Sequence semi-automatic genome annotation), which provides comprehensive computational tools and methods for rapid, highquality insertion sequence (IS) annotation

Summary

Introduction

The growing number of completely sequenced bacterial and archaeal genomes are making important contributions to understanding genome structure and evolution. Annotation of gene content and genome comparison have provided much valuable information and key insights into how prokaryotes are genetically tailored to their lifestyles. The rate at which sequenced prokaryotic genomes and metagenomes are accumulating is constantly increasing with the development of new high-throughput sequencing techniques. The resulting mass of data should provide an unparalleled opportunity to achieve a better understanding of prokaryotes. High quality genome annotation together with a standardized nomenclature is an essential requirement for this since most proteins identified from these sequencing projects will probably never be characterized biochemically [1]. Expert genome annotation is fast becoming a bottleneck in genomics [2]

Methods

Results

Conclusion