Protein multiple sequence alignment using knowledge

The authors have developed an alignment system composed of two modules: the aligner and the intelligent refiner. The aligner produces a computationally optimal or semioptimal alignment. Then the intelligent refiner refines the product of the aligner to produce the biologically optimal or meaningful alignment. To design an intelligent refiner, the authors interviewed experts on multiple alignment, and extracted the knowledge they use to align sequences. The algorithm system introduced produces biologically meaningful alignment by iteratively applying the alignment rules that were extracted. Examples of application of the intelligent refiner are given.