Data mining pathogen genomes using GeneOrder and CoreGenes and CGUG: gene order, synteny and in silico proteomes.
Sequence databases are growing exponentially due to 'next generation' DNA analysers and applications of these data. Databases include multiple sequences of previously sequenced organisms, particularly ones of consequence to human health. Applications are limited by tools available to mine them, particularly user-friendly tools that are useful for bench researchers. GeneOrder, CoreGenes and CGUG are web-based 'on-the-fly' tools that examine gene order and synteny, as well as proteomes for comparative genomics and for drug discovery and design targets. CoreGenes (CGUG) now allows analysis of genomes ranging up to 1.9 megabases. Many of these small genome bacteria have impacts on human health.
Mahadevan
Padmanabhan
P
Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA. E-mail: padmahadevan@gmail.com. padmahadevan@gmail.com
King
John F
JF
Seto
Donald
D
D000465:Algorithms; D001419:Bacteria / Q000235:genetics / Q000472:pathogenicity; D019295:Computational Biology; D003198:Computer Simulation; D030561:Databases, Nucleic Acid / Q000706:statistics & numerical data*; D048168:Escherichia coli K12 / Q000235:genetics; D019453:Escherichia coli O157 / Q000235:genetics / Q000472:pathogenicity; D023061:Gene Order; D023281:Genomics / Q000706:statistics & numerical data; D006801:Humans; D008957:Models, Genetic; D040901:Proteomics / Q000706:statistics & numerical data; D045473:Severe acute respiratory syndrome-related coronavirus / Q000235:genetics / Q000472:pathogenicity; D012485:Salmonella typhi / Q000235:genetics / Q000472:pathogenicity; D016415:Sequence Alignment / Q000706:statistics & numerical data; D012984:Software; D026801:Synteny; D014780:Viruses / Q000235:genetics / Q000472:pathogenicity