METHODS FOR COMPARING A DNA-SEQUENCE WITH A PROTEIN-SEQUENCE

We describe two methods for constructing an optimal global alignment o f and an optimal local alignment between a DNA sequence and a protein sequence. The alignment model of the methods addresses the problems of frameshifts and introns in the DNA sequence. The methods require comp uter memory proportional to the sequence lengths, so they can rigorous ly process very huge sequences. The simplified versions of the methods were implemented as computer programs named NAP and LAP. The experime ntal results demonstrate that the programs are sensitive and powerful tools for finding genes by DNA-protein sequence homology.