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AbsractProtein sequence alignment is an important technique for drawing phylogenic trees and predicting the structure and function of proteins. So far, many alignment systems have been developed. These systems produce optimal or near-optimal alignment according to an art zficiall y defined e vu lu at i o n fun ct io n . How ever, these computationally optimal alignments don't necessarily correspond t o the biologically optimal alignment that biologists desire.We interviewed experts on alignment and extracled the knowledge they use to align sequences. The alagnment system we will introduce in this paper produces biologically meaningful (sometimes optimal) alignment b y iteratively applying the alignment rules that we extracted.