PMAP II

Resolve pathway mapping problem with Operon and
Regulon information by Integer Programming

I agree and want to go to the PMAP II online server

  1. Please cite this paper if you use this online server for your publication:
    • F. Mao, Z. Su, V. Olman, P. Dam, Z. Liu, Ying Xu, "Mapping of orthologous genes in the context of biological pathways: an application of integer programming", Proc Natl Acad Sci USA, 103 (1): 129-134, 2006.
  2. To do more complicated computing, please download the whole package of PMAP II.
  3. All operon files are pre-calculated and stored on the server, please cite this two paper for operon prediction algorithm:
    • X. Chen, Z. Su, Ying Xu and T Jiang, "Computational Prediction of Operons in Synechococcus sp WH8102", Proceedings of 15th International Conference on Genome Informatics, pp 211 - 222, 2004 (Best paper award of GIW04).
    • X. Chen, Z. Su, P. Dam, B. Palenik, Ying Xu, and T. Jiang, Operon prediction by comparative genomics: an application to the Synechococcus WH8102 genome, Nucleic Acids Research, Vol32 (7), 2147 - 2157,2004.
  4. No regulon files are available on the server.
  5. Please download PMAP II package and run it in your own computer if you want to supply your own operon and regulon file.
  6. Currently you can specify the template genome as one of 198 bacteria genomes we stored on the server and the target genome as one of the 144 genomes we have calculated the operons for.
  7. If you want to specify your own template genome and target genome, please download the PMAP II package.
I agree and want to go to the PMAP II online server