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CAAT-Box, Contigs-Assembly and Annotation Tool-Box for genome sequencing projects.

L Frangeul1, P Glaser, C Rusniok

  • 1Génopole, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris 15, France. lfrangeu@pasteur.fr

Bioinformatics (Oxford, England)
|January 31, 2004
PubMed
Summary

The Contigs-Assembly and Annotation Tool-Box (CAAT-Box) software aids genome projects by predicting contig links and enabling early genome annotation. This tool facilitates efficient gene-oriented annotation during genome assembly.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Genome projects utilizing shotgun sequencing strategies require robust computational tools for assembly and annotation.
  • Existing tools may not adequately support annotation during the genome's finishing phase.

Purpose of the Study:

  • To introduce the Contigs-Assembly and Annotation Tool-Box (CAAT-Box) software package.
  • To provide novel tools for predicting contig links and initiating genome annotation during the finishing phase.

Main Methods:

  • CAAT-Box employs similarity searches against whole genome sequences to predict contig links.
  • It generates Individual Protein files (IPFs) for each Open Reading Frame (ORF), including flanking sequence for annotation.
  • IPFs support integrated automatic and manual annotation, with updates based on modified sequences after re-assembly.

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Main Results:

  • CAAT-Box was successfully utilized to assemble and annotate complete genomes, including Listeria monocytogenes and Streptococcus agalactiae.
  • The software enables a gene-oriented annotation strategy, allowing annotation to commence early in the genome project.

Conclusions:

  • CAAT-Box offers an efficient approach to genome annotation by managing Individual Protein files independently of assembly progression.
  • The web-accessible nature of IPFs facilitates collaborative annotation efforts among different research groups.