Introduction

We have implemented a genome annotation system for prokaryotes called AGMIAL. Our approach embodies a number of key principles. First, expert manual annotators are seen as a critical component of the overall system; user interfaces were cyclically refined to satisfy their needs. Second, the overall process should be orchestrated in terms of a global annotation strategy; this facilitates coordination between a team of annotators and automatic data analysis. Third, the annotation strategy should allow progressive and incremental annotation from a time when only a few draft contigs are available, to when a final finished assembly is produced. The overall architecture employed is modular and extensible, being based on the W3 standard Web services framework. Specialized modules interact with two independent core modules that are used to annotate, respectively, genomic and protein sequences. AGMIAL is currently being used by several INRA laboratories to analyze genomes of bacteria relevant to the food-processing industry, and is distributed under an open source license.

Publications

  1. AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system.
    Cite this
    Bryson K, Loux V, Bossy R, Nicolas P, Chaillou S, van de Guchte M, Penaud S, Maguin E, Hoebeke M, Bessières P, Gibrat JF, 2006-01-01 - Nucleic acids research

Credits

  1. K Bryson
    Developer

  2. V Loux
    Developer

  3. R Bossy
    Developer

  4. P Nicolas
    Developer

  5. S Chaillou
    Developer

  6. M van de Guchte
    Developer

  7. S Penaud
    Developer

  8. E Maguin
    Developer

  9. M Hoebeke
    Developer

  10. P Bessières
    Developer

  11. J-F Gibrat
    Investigator

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Summary
AccessionBT000183
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByJ-F Gibrat