BEST

BEST is a suite of motif-finding programs, including four motif-finding programs: AlignACE, BioProspector, Consensus, MEME, and the optimization program BioOptimizer configured for each of these programs.

• Dongsheng Che, S. Jensen, L. Cai and J.S. Liu. BEST: binding-site estimation suite of tools. Bioinformatics, 2005, 21(12):2909-2911. [ | pdf ]

GIDetector

GIDetector is a software that is used to detect genomic islands in prokaryotic genomes. GIDetector collects prokaryotic genome data from public websites based on users' specification, analyzes genome features using multiple sources, including embedded third-party software Alien_hunter and REPuter, and predict genomic islands based on our trained models, which are decision-tree based ensemble classifiers.

• Dongsheng Che, C. Hockenbury, R. Marmelsteinand and K. Rasheed. Classification of Genomic Islands Using Decision-tree Based Algorithms [ ]

OperonDT

OperonDT is an operon predictor using decision tree approach. OperonDT mainly uses three kinds of features: intergenic distance, COG pattern and gene order conservation to build tree models.

• Che D., Zhao, J., Cai, L. and Xu, Y., Operon Prediction in Microbial Genomes Using Decision Tree Approach. Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2007), pp 135-142.

   

• Che D., Zhao, J., Cai, L. and Xu, Y. Decision Tree Modeling Predicts Operon Structures of Prokaryotic Genomes. International Journal of Information Technology and Intelligent Computing (in press).

Uber-OperonDB

Uber-OperonDB cantains 91 predicted genome-scale uber-operons in 91 prokaryotic genomes.

• Dongsheng Che, G. Li, F. Mao, H. Wu and Y. Xu. Detecting uber-operons in prokaryotic genomes. Nucleic Acids Res. 34(8):2418-2427 [ | pdf ]

UNIPOP

UNIversal Predictor of OPerons (UNIPOP) cantains 365 predicted genome-scale operons.

• G. Li, Dongsheng Che and Y. Xu. A Universal and Accurate Operon Predictor for All Prokaryotic Genomes. Journal of Bioinformatics and Computational Biology, 7(1):19-38 [ | pdf ]