A computer program to compare sequence fingerprints of homologous proteinsfor the rapid assessment of their primary structure differences

We have developed a computer program for the rapid assessment of the primar y structure differences between a protein of unknown sequence and a homolog ous known protein. Both proteins are reduced, alkylated, and digested with the same hydrolytic agent. The unfractionated peptide mixtures are submitte d to automatic sequence analysis. Based on the knowledge of the reference s equence, the program utilizes the analysis data to identify all the potenti al peptides present in the two mixtures, determining their primary structur e, homology degree, and molecular weight calculated both as integer MH+ and average mass variables. These fingerprints allow the user to easily identi fy the structural differences between the mio proteins and clarify possible doubts by a mass spectrometric analysis of the two mixtures. In order to v erify the utility of the program, we provide an application example using t he already reported data of two homologous proteins.