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Genet Mol Res. 2005 Sep 30;4(3):571-80.

An agent-based system for re-annotation of genomes.

Author information

  • 1Instituto de Inform├ítica, Universidade Federal do Rio Grande do Sul, Caixa Postal 15064, 90501-970 Porto Alegre, RS, Brazil. lvnascimento@inf.ufrgs.br

Abstract

Genome annotation projects can produce incorrect results if they are based on obsolete data or inappropriate models. We have developed an automatic re-annotation system that uses agents to perform repetitive tasks and reports the results to the user. These tasks involve BLAST searches on biological databases (GenBank) and the use of detection tools (Genemark and Glimmer) to identify new open reading frames. Several agents execute these tools and combine their results to produce a list of open reading frames that is sent back to the user. Our goal was to reduce the manual work, executing most tasks automatically by computational tools. A prototype was implemented and validated using Mycoplasma pneumoniae and Haemophilus influenzae original annotated genomes. The results reported by the system identify most of new features present in the re-annotated versions of these genomes.

PMID:
16342042
[PubMed - indexed for MEDLINE]
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