AGMIAL:: implementing an annotation strategy for prokaryote genomes as a distributed system

被引：75

作者：

Bryson, K.

Loux, V.

Bossy, R.

Nicolas, P.

Chaillou, S.

van de Guchte, M.

Penaud, S.

Maguin, E.

Hoebeke, M.

Bessieres, P.

Gibrat, J-F ^{[1
]}

机构：

[1] INRA, Math Informat & Genome, F-78352 Jouy En Josas, France

[2] INRA, Flore Lact & Environm Carne, F-78352 Jouy En Josas, France

[3] INRA, Genet Microbienne, F-78352 Jouy En Josas, France

来源：

NUCLEIC ACIDS RESEARCH | 2006年 / 34卷 / 12期

关键词：

D O I：

10.1093/nar/gkl471

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 [生物化学与分子生物学]; 081704 [应用化学];

摘要：

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.

引用

页码：3533 / 3545

页数：13

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