In the wake of large genome sequencing projects, the rapid development of laboratory techniques have resulted in a huge scaling up of data production. The amount of sequence data is growing rapidly and so is the need to include more data into biological analysis processes. Large scale research is carried out in many different levels including genome, proteome, transcriptome, and metabolome levels, rapidly increasing the wealth of data. Therefore, the most important challenge facing the molecular biology today is to make sense of this mass of data. Our interest is in developing computer tools and algorithms that allow extraction of useful biological information - in particular finding biologically meaningful solutions to NP-complete problems with a reasonable amount of computation.