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Searching for frameshift evolutionary relationships between protein sequence families
Author(s) -
Pellegrini Matteo,
Yeates Todd O.
Publication year - 1999
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(19991101)37:2<278::aid-prot12>3.0.co;2-x
Subject(s) - frameshift mutation , translation (biology) , sequence (biology) , protein evolution , homology (biology) , computational biology , genetics , protein sequencing , sequence alignment , biology , database , peptide sequence , computer science , amino acid , phenotype , gene , messenger rna
The protein sequence database was analyzed for evidence that some distinct sequence families might be distantly related in evolution by changes in frame of translation. Sequences were compared using special amino acid substitution matrices for the alternate frames of translation. The statistical significance of alignment scores were computed in the true database and shuffled versions of the database that preserve any potential codon bias. The comparison of results from these two databases provides a very sensitive method for detecting remote relationships. We find a weak but measurable relatedness within the database as a whole, supporting the notion that some proteins may have evolved from others through changes in frame of translation. We also quantify residual homology in the ordinary sense within a database of generally unrelated sequences. Proteins 1999;37:278–283. ©1999 Wiley‐Liss, Inc.