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CoGenT++: an extensive and extensible data environment for computational genomics

Goldovsky, Leon; Janssen, Paul; Ahrén, Dag LU ; Audit, Benjamin; Cases, Ildefonso; Darzentas, Nikos; Enright, Anton; López-Bigas, Núria; Peregrin-Alvarez, José and Smith, Mike, et al. (2005) In Bioinformatics 21(19). p.3806-3810
Abstract
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... (More)
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@ebi.ac.uk (Less)
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organization
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Contribution to journal
publication status
published
subject
in
Bioinformatics
volume
21
issue
19
pages
3806 - 3810
publisher
Oxford University Press
external identifiers
  • scopus:27544465780
ISSN
1367-4803
DOI
10.1093/bioinformatics/bti579
language
English
LU publication?
no
id
de944621-256e-4ee5-b0b9-ddc188060025 (old id 952268)
date added to LUP
2008-01-31 14:07:48
date last changed
2017-01-01 04:59:38
@article{de944621-256e-4ee5-b0b9-ddc188060025,
  abstract     = {Motivation: CoGenT++ is a data environment for computational research in comparative and functional genomics, designed to address issues of consistency, reproducibility, scalability and accessibility. <br/><br>
<br/><br>
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. <br/><br>
<br/><br>
Conclusion: CoGenT++ provides a comprehensive environment for computational genomics, accessible primarily for large-scale analyses as well as manual browsing. <br/><br>
<br/><br>
Availability: The database and component downloads are accessible at http://cgg.ebi.ac.uk/cogentpp.html. <br/><br>
<br/><br>
Contact: ouzounis@ebi.ac.uk},
  author       = {Goldovsky, Leon and Janssen, Paul and Ahrén, Dag and Audit, Benjamin and Cases, Ildefonso and Darzentas, Nikos and Enright, Anton and López-Bigas, Núria and Peregrin-Alvarez, José and Smith, Mike and Tsoka, Sophia and Kunin, Victor and Ouzounis, Christos},
  issn         = {1367-4803},
  language     = {eng},
  number       = {19},
  pages        = {3806--3810},
  publisher    = {Oxford University Press},
  series       = {Bioinformatics},
  title        = {CoGenT++: an extensive and extensible data environment for computational genomics},
  url          = {http://dx.doi.org/10.1093/bioinformatics/bti579},
  volume       = {21},
  year         = {2005},
}