ISsaga - Semi-Automatic IS Annotation
ISsaga - IS Semi-automatic Genomic Annotation

About

The in-depth analysis of the growing number of completely sequenced prokaryotic genomes is providing important contributions to our understanding the biological world. Large-scale sequencing of prokaryotic genomes demands automation of certain annotation tasks, such as prediction of coding sequences and promoters. But automatic processes are severely limited and can lead to poor quality annotation at the DNA level. A crucial example of this are the mobile genetic elements (MGE) which have played a major role in genome evolution and contribute massively to horizontal gene transfer. A detailed and accurate analysis of MGE content and distribution would provide an important picture of the evolution of their host genomes. Unfortunately, a majority of bacterial and archeal genome sequences deposited in the public databases are seriously compromised in their MGE annotation, particularly for ISs, one of the simplest autonomous MGEs found. In particular fragments of incomplete ISs which represent the scars of previous recombination events are rarely annotated but provide important information on genome evolution.
To facilitate the annotation of these elements, ISsaga provides a high-quality semi-automatic annotation system, directed to the accurate identification and annotation of ISs.


Main Recomendations

  • Web-browser:
  • Firefox 2.0 or newer, Google Chrome, Safari 4.0 or newer, and Opera 10 or newer. With the latest version of the Java and Flash plug-in, and javascript enabled.
  • Genome File:
  • ISsaga accepts two main inputs, GenBank and FASTA files.
    The recomended genome input file for ISsaga is the GenBank file format.
    The GenBank file must have the (.gbk) extension, and the FASTA files must have (.fasta) for nucleotides and (.faa) for proteins.
  • Annotation Process:
  • The semi-automatic step works at two levels (protein annotation level and nucleotide annotation level).

    The protein annotation level is the first step, and will process the genome file, given by the user. The result of this process is a pie chart with the transposase distribution in the given genome.
    The nucleotide annotation level is the second step, and will identify complete and/or partial ISs, showing the predicted number of candidates in the semi-automatic -> List annotated IS(s) menu. This report will show a button to be pressed by the user, in order to start the identification.The result of this process will be a report of each identified IS.


    link
    ISsaga Manual (Version 1.0) (PDF Download) ISsaga Poster (2010)
    (PDF Download)


    Credits

    ISsaga annotation tool was conceived and designed by Alessandro Varani, with the help of Patricia Siguier, Edith Gourbeyre and Mike Chandler. All the graphics and web-design was provide by David Villa.

    The annotation database was created using data provided by members of the Mobile Genetic Elements team (Laboratoire  de Microbiologie et Génétique Moléculaire, CNRS, UMR5100,Université Paul Sabatier, Toulouse, FRANCE).

    ISsaga 2.0 is powered by:

  • BioPerl - Collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.
  • Kraken - Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
  • Prokka - Prokka is a software tool for the rapid annotation of prokaryotic genomes.
  • OASIS - Optimized Annotation System for Insertion Sequences.
  • BLAST - Basic Local Alignment Search Tool.
  • EMBOSS - The European Molecular Biology Open Software Suite.
  • MySQL - Relational database management system (RDBMS).
  • phpMyEdit - Instant MySQL Table Editor and PHP Code Generator.
  • Sequence Manipulation Suite - Collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences.
  • CGView - Java package for generating high quality, zoomable maps of circular genomes.
  • AmCharts - Fully customizable animated, 3D or 2D flash charts.
  • Jalview - Multiple alignment editor.
  • Readseq - Read & reformat biosequences.

  • ISfinder team
    - ISsaga developer
    - ISfinder curator and management
    - ISfinder curator
    - ISfinder coordinator


    ISfinder Webmaster :
    Network and System manager :
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    Support

    This work was supported by Capes Foundation, Ministry of Education of Brazil.
    Grant Number: 2497-08-5

    This work was supported by C.N.R.S (Centre national de la recherche scientifique) and IBiSa (Infrastructures en Biologie Sante et Agronomie)