Does protein relatedness require sequence matching? Alignment via networks in sequence space.
To establish possible function of a newly discovered protein, alignment of its sequence with other known sequences is required. When the similarity is marginal, the function remains uncertain. A principally new approach is suggested: to use networks in the protein sequence space. The functionality of the protein is firmly established via networks forming chains of consecutive pair-wise matching fragments. The distant relatives are, thus, considered as relatives, though in some cases, there is even no sequence match between the ends of the chain, while the entire chain belongs to the same functional and structural network.
Frenkel
Zakharia M
ZM
Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel. zakharf@research.haifa.ac.il
D000465:Algorithms; D000595:Amino Acid Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
D011506:Proteins