CoGenT++: an extensive and extensible data environment for computational genomics
Author
Summary, in English
Motivation: CoGenT++ is a data environment for computational research in comparative and functional genomics, designed to address issues of consistency, reproducibility, scalability and accessibility.
Description: CoGenT++ facilitates the re-distribution of all fully sequenced and published genomes, storing information about species, gene names and protein sequences. We describe our scalable implementation of ProXSim, a continually updated all-against-all similarity database, which stores pairwise relationships between all genome sequences. Based on these similarities, derived databases are generated for gene fusions—AllFuse, putative orthologs—OFAM, protein families—TRIBES, phylogenetic profiles—ProfUse and phylogenetic trees. Extensions based on the CoGenT++ environment include disease gene prediction, pattern discovery, automated domain detection, genome annotation and ancestral reconstruction.
Conclusion: CoGenT++ provides a comprehensive environment for computational genomics, accessible primarily for large-scale analyses as well as manual browsing.
Availability: The database and component downloads are accessible at http://cgg.ebi.ac.uk/cogentpp.html.
Contact: ouzounis [at] ebi [dot] ac [dot] uk
Description: CoGenT++ facilitates the re-distribution of all fully sequenced and published genomes, storing information about species, gene names and protein sequences. We describe our scalable implementation of ProXSim, a continually updated all-against-all similarity database, which stores pairwise relationships between all genome sequences. Based on these similarities, derived databases are generated for gene fusions—AllFuse, putative orthologs—OFAM, protein families—TRIBES, phylogenetic profiles—ProfUse and phylogenetic trees. Extensions based on the CoGenT++ environment include disease gene prediction, pattern discovery, automated domain detection, genome annotation and ancestral reconstruction.
Conclusion: CoGenT++ provides a comprehensive environment for computational genomics, accessible primarily for large-scale analyses as well as manual browsing.
Availability: The database and component downloads are accessible at http://cgg.ebi.ac.uk/cogentpp.html.
Contact: ouzounis [at] ebi [dot] ac [dot] uk
Department/s
Publishing year
2005
Language
English
Pages
3806-3810
Publication/Series
Bioinformatics
Volume
21
Issue
19
Document type
Journal article
Publisher
Oxford University Press
Topic
- Bioinformatics and Systems Biology
Status
Published
Research group
- Microbial Ecology
ISBN/ISSN/Other
- ISSN: 1367-4803