Abstract:
: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.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Bryson K,Loux V,Bossy R,Nicolas P,Chaillou S,van de Guchte M,Penaud S,Maguin E,Hoebeke M,Bessières P,Gibrat JFdoi
10.1093/nar/gkl471subject
Has Abstractpub_date
2006-07-19 00:00:00pages
3533-45issue
12eissn
0305-1048issn
1362-4962pii
34/12/3533journal_volume
34pub_type
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