ArticleBMC bioinformatics2005
FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
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- Noncontiguous finished genome sequences and description ofNew microbes and new infections · 2018Article
- Anaerococcus jeddahensis sp. nov., a New Bacterial Species Isolated From Healthy Nomadic Bedouin Woman From Saudi Arabia.Current microbiology · 2018Article
- Eggerthella timonensis sp. nov, a new species isolated from the stool sample of a pygmy female.MicrobiologyOpen · 2018Article
- Genomic and phenotypic description of the newly isolated human species Collinsella bouchesdurhonensis sp. nov.MicrobiologyOpen · 2018Article
- Draft Genome and Description of Eisenbergiella massiliensis Strain AT11Current microbiology · 2018Article
- Noncontiguous finished genome sequences and descriptions ofNew microbes and new infections · 2018Article
- Characterization of a novel Gram-stain-positive anaerobic coccus isolated from the female genital tract: Genome sequence and description of Murdochiella vaginalis sp. nov.MicrobiologyOpen · 2018Article
- Microbial culturomics to isolate halophilic bacteria from table salt: genome sequence and description of the moderately halophilic bacteriumNew microbes and new infections · 2018Article
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- Taxonogenomic description of four newNew microbes and new infections · 2018Article
- Noncontiguous finished genome sequence and description ofNew microbes and new infections · 2018Article
- Noncontiguous finished genome sequences and descriptions ofNew microbes and new infections · 2017Article
- Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life.Genes · 2017Article
- Noncontiguous finished genome sequences and description ofNew microbes and new infections · 2017Article
- Genome sequence and description ofNew microbes and new infections · 2017Article
5 more citing papers are in PubMed but not listed here.
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundTwo of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes). Structural and functional annotation both require the complex chaining of numerous different software, algorithms and methods under the supervision of a biologist. The automation of these pipelines is necessary to manage huge amounts of data released by sequencing projects. Several pipelines already automate some of these complex chaining but still necessitate an important contribution of biologists for supervising and controlling the results at various steps.
resultsHere we propose an innovative automated platform, FIGENIX, which includes an expert system capable to substitute to human expertise at several key steps. FIGENIX currently automates complex pipelines of structural and functional annotation under the supervision of the expert system (which allows for example to make key decisions, check intermediate results or refine the dataset). The quality of the results produced by FIGENIX is comparable to those obtained by expert biologists with a drastic gain in terms of time costs and avoidance of errors due to the human manipulation of data.
conclusionThe core engine and expert system of the FIGENIX platform currently handle complex annotation processes of broad interest for the genomic community. They could be easily adapted to new, or more specialized pipelines, such as for example the annotation of miRNAs, the classification of complex multigenic families, annotation of regulatory elements and other genomic features of interest.
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