Table 3.
Genome (re‐)annotation pipelines.
| Pipeline | Organization | Description | Access/distribution | Reference |
|---|---|---|---|---|
| IGS | University of Maryland | A FREE resource for genomics researchers and educators bringing advanced bioinformatics tools to the lab bench and the classroom | http://ae.igs.umaryland.edu/cgi/index.cgi Free service | None |
| JCVI annotation service | J. Craig Venter Institute (JCVI) | Free to use genome annotation service | http://www.jcvi.org/cms/research/projects/annotation‐service/overview/ Free to use annotation service | None |
| MiGAP | Database Center for Life Sciences (DBCLS) | Microbial Genome Annotation Pipeline (MiGAP) for diverse users | http://migap.lifesciencedb.jp/ Note: site is in Japanese | http://www.jsbi.org/modules/journal1/index.php/GIW09/Poster/GIW09S001.pdf |
| MaGe/MicroScope | GENOSCOPE | Magnifying Genomes: microbial genome annotation system | http://www.genoscope.cns.fr/agc/mage Free service | Vallenet et al. (2006); Vallenet et al. (2009) |
| BASys | University of Alberta, Canada | A web server for bacterial genome annotation | http://wishart.biology.ualberta.ca/basys/ Free to use | Van Domselaar et al. (2005) |
| RAST | Fellowship for Integration of Genomes (FIG) | The RAST Server: Rapid Annotations using Subsystems Technology based on the Seed | http://rast.nmpdr.org/ Free to use service | Aziz et al. (2008) |
| xBASE | University of Birmingham, UK | Bacterial genome annotation service | http://xbase.ac.uk/annotation/ Free to use service | Chaudhuri et al. (2008) |
| IMG ER | Joint Genome Institute (JGI) | A system for microbial genome annotation expert review and curation | http://img.jgi.doe.gov/er Free service | Markowitz et al. (2009) |
| GenVar | Virginia Bioinformatics Institute | Bacterial gene annotation and comparative genomics pipeline | http://patric.vbi.vt.edu/downloads/software/GenVar Free for non‐commercial use | Yu et al. (2007) |
| Pedant‐Pro | Biomax | Genome analysis package for comprehensive analysis of DNA and protein sequences | http://www.biomax.de/products/pedantpro.php Commercial license | Frishman et al. (2001) |
| AGMIAL | INRA, France | An annotation strategy for prokaryote genomes as a distributed system | http://genome.jouy.inra.fr/agmial/ Open source license | Bryson et al. (2006) |
| GenDB | CeBiTec, Germany | Bacterial annotation system | http://www.cebitec.uni‐bielefeld.de/groups/brf/software/gendb_info/ Free to use, stand‐alone software | Meyer et al. (2003) |
| DIYA | DIY Genomics Consortium | A bacterial annotation pipeline for any genomics lab | https://sourceforge.net/projects/diyg/ Free to use, stand‐alone software | Stewart et al. (2009) |
| SABIA | LNCC, Brazil | Bacterial annotation system | http://www.sabia.lncc.br/ Free to use, stand‐alone software | Almeida et al. (2004) |
| MAGPIE | Genome Prairie Project, Canada | Genome annotation system | http://magpie.ucalgary.ca/ Free to use, stand‐alone software | Gaasterland and Sensen (1996) |
| Restauro‐G | Institute for Advanced Biosciences, Keio University | A Rapid Genome Re‐Annotation System for Comparative Genomics | http://restauro‐g.iab.keio.ac.jp/ Software distributed under the GNU public license | Tamaki et al. (2007) |
| ATUCG system | Universidade Federal do Rio Grande do Sul, Brasil | Agent‐based environment for automatic annotation of Genomes | None Software should be requested at authors | Nascimento and Bazzan (2005) |
| Taverna: annotation of genomes | University of Manchester | Interactive genome annotation pipeline. | http://www.taverna.org.uk/introduction/taverna‐in‐use/annotation/annotation‐of‐genomes/ | Hull et al. (2006) |
| KAAS | Kyoto Encyclopedia for Genes and Genomes (KEGG) | KEGG automated annotation service for metabolic pathways | http://www.genome.jp/tools/kaas/ Free to use service | Moriya et al. (2007) |