Bryson, K.;
Loux, V.;
Bossy, R.;
Nicolas, P.;
Chaillou, S.;
van de Guchte, M.;
Penaud, S.;
... Gibrat, J.-F.; + view all
(2006)
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system.
Nucleic Acids Research
, 34
(12)
pp. 3533-3545.
10.1093/nar/gkl471.
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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.
| Type: | Article |
|---|---|
| Title: | AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1093/nar/gkl471 |
| Publisher version: | http://dx.doi.org/10.1093/nar/gkl471 |
| Language: | English |
| Additional information: | © 2006 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| URI: | https://discovery.ucl.ac.uk/id/eprint/13258 |
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