A new algorithm for analysis of the homology in protein primary structure.
A new algorithm for analysis of the homology and genetic semihomology in protein sequence is described. It assumes the close relation between the compared amino acids and their codons in related proteins. The algorithm is based on the network of the genetic relationship between amino acids and, thus differs from the commonly used statistical matrices. The results obtained by using this method are more comprehensive than used at present, and reflect the actual mechanism of protein differentiation and evolution. They concern: (1) location of homologous and semihomologous sites in compared proteins; (2) precise estimation of insertion/deletion gaps in non-homologous fragments; (3) analysis of internal homology and semihomology; (4) precise location of domains in multidomain proteins; (5) estimation of genetic code of non-homologous fragments; (6) construction of genetic probes; (7) studies on differentiation processes among related proteins; (8) estimation of the degree of relationship among related proteins; (9) studies on the evolution mechanism within homologous protein families and (10) confirmation of actual relationship of sequences showing low degree of homology.
Leluk
J
J
Institute of Biochemistry and Molecular Biology, University of Wrocław, Poland. lulu@bf.uni.wroc.pl
D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000235:genetics; D000818:Animals; D001200:Ascaris; D001483:Base Sequence; D001516:Bees; D002645:Chickens; D003198:Computer Simulation; D015387:Egg Proteins, Dietary; D008969:Molecular Sequence Data; D010059:Ovomucin / Q000737:chemistry; D010446:Peptide Fragments / Q000737:chemistry; D011480:Protease Inhibitors / Q000737:chemistry; D011487:Protein Conformation; D015865:Racquet Sports; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid
D000596:Amino Acids; D015387:Egg Proteins, Dietary; D010446:Peptide Fragments; D011480:Protease Inhibitors; D010059:Ovomucin; C004224:ovoinhibitor