AGMIAL: Implementing an Annotation Strategy for Prokaryote Genomes As a Distributed System

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2006 Jul 21

PMID 16855290

Citations 58

Authors

K Bryson

V Loux

R Bossy

P Nicolas

S Chaillou

M van de Guchte

S Penaud

E Maguin

M Hoebeke

P Bessieres

J-F Gibrat

Affiliations

Soon will be listed here.

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.

Citing Articles

Draft Genome Sequence of the Lignocellulolytic and Thermophilic Bacterium Thermobacillus xylanilyticus XE.

Rakotoarivonina H, Loux V, Doliwa C, Martin V, Remond C Microbiol Resour Announc. 2022; 11(4):e0093421.

PMID: 35258325 PMC: 9022518. DOI: 10.1128/mra.00934-21.

Complete Genome Sequence of the Industrial Fast-Acidifying Strain Streptococcus thermophilus N4L.

Proust L, Loux V, Martin V, Magnabosco C, Pedersen M, Monnet V Microbiol Resour Announc. 2018; 7(8).

PMID: 30533920 PMC: 6256512. DOI: 10.1128/MRA.01029-18.

Complete and Draft Genome Sequences of Nine Lactobacillus sakei Strains Selected from the Three Known Phylogenetic Lineages and Their Main Clonal Complexes.

Loux V, Coeuret G, Zagorec M, Verges M, Chaillou S Genome Announc. 2018; 6(16).

PMID: 29674528 PMC: 5908949. DOI: 10.1128/genomeA.00082-18.

Surface Protein SlpB Is Involved in Adhesion to Intestinal HT-29 Cells.

do Carmo F, Rabah H, Huang S, Gaucher F, Deplanche M, Dutertre S Front Microbiol. 2017; 8:1033.

PMID: 28642747 PMC: 5462946. DOI: 10.3389/fmicb.2017.01033.

Whole-Genome Sequencing of Seven Strains of Staphylococcus lugdunensis Allows Identification of Mobile Genetic Elements.

Argemi X, Martin V, Loux V, Dahyot S, Lebeurre J, Guffroy A Genome Biol Evol. 2017; 9(5).

PMID: 28444231 PMC: 5425232. DOI: 10.1093/gbe/evx077.

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