CoGenT++: an extensive and extensible data environment for computational genomics.
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.
Goldovsky
Leon
L
Computational Genomics Group, The European Bioinformatics Institute EMBL, Cambridge Outstation, Cambridge CB10 1SD, UK.
Janssen
Paul
P
Ahrén
Dag
D
Audit
Benjamin
B
Cases
Ildefonso
I
Darzentas
Nikos
N
Enright
Anton J
AJ
López-Bigas
Núria
N
Peregrin-Alvarez
José M
JM
Smith
Mike
M
Tsoka
Sophia
S
Kunin
Victor
V
Ouzounis
Christos A
CA
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