title: CoGenT++: an extensive and extensible data environment for computational genomics.
abstract: BACKGROUND
  CoGenT++ is a data environment for computational research in comparative and functional genomics, designed to address issues of consistency, reproducibility, scalability and accessibility.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  CoGenT++ provides a comprehensive environment for computational genomics, accessible primarily for large-scale analyses as well as manual browsing.
authors.affiliation: Computational Genomics Group, The European Bioinformatics Institute EMBL, Cambridge Outstation, Cambridge CB10 1SD, UK.
authors.forename: Leon
authors.initials: L
authors.lastname: Goldovsky
authors.forename: Paul
authors.initials: P
authors.lastname: Janssen
authors.forename: Dag
authors.initials: D
authors.lastname: Ahrén
authors.forename: Benjamin
authors.initials: B
authors.lastname: Audit
authors.forename: Ildefonso
authors.initials: I
authors.lastname: Cases
authors.forename: Nikos
authors.initials: N
authors.lastname: Darzentas
authors.forename: Anton J
authors.initials: AJ
authors.lastname: Enright
authors.forename: Núria
authors.initials: N
authors.lastname: López-Bigas
authors.forename: José M
authors.initials: JM
authors.lastname: Peregrin-Alvarez
authors.forename: Mike
authors.initials: M
authors.lastname: Smith
authors.forename: Sophia
authors.initials: S
authors.lastname: Tsoka
authors.forename: Victor
authors.initials: V
authors.lastname: Kunin
authors.forename: Christos A
authors.initials: CA
authors.lastname: Ouzounis
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods; D003196:Computer Graphics; D003628:Database Management Systems; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods; D017421:Sequence Analysis / Q000379:methods*; D012984:Software; D018511:Systems Integration; D014584:User-Computer Interface