Screening synteny blocks in pairwise genome comparisons through integer programming.
Haibao TangEric LyonsBrent S. PedersenJames C. SchnableAndrew H. PatersonMichael FreelingPublished in: BMC Bioinform. (2011)
Keyphrases
- integer programming
- pairwise
- comparative genomics
- sequence alignment
- np hard
- ai planning
- network flow
- linear programming
- constraint programming
- production planning
- cutting plane algorithm
- column generation
- similarity measure
- sequence data
- markov random field
- integer program
- facility location
- set covering
- lagrangian relaxation
- cutting plane
- gene clusters
- evolutionary history
- transportation problem
- vehicle routing problem with time windows
- round robin tournament
- dantzig wolfe decomposition
- integer programming formulations
- belief propagation
- gene expression analysis
- valid inequalities
- loss function
- upper bound
- reinforcement learning