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Oligopeptide biases in protein sequences and their use in predicting protein coding regions in nucleotide sequences
Author(s) -
McCaldon Peter,
Argos Patrick
Publication year - 1988
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/prot.340040204
Subject(s) - oligopeptide , computational biology , homology (biology) , biology , genetics , coding region , nucleotide , sequence (biology) , protein sequencing , amino acid , peptide sequence , peptide , gene , biochemistry
We have examined oligopeptides with lengths ranging from 2 to 11 residues in protein sequences that show no obvious evolutionary relationship. All sequences in the Protein Identification Resource database were carefully classified by sensitive homology searches into superfamilies to obtain unbiased oligopeptide counts. The results, contrary to previous studies, show clear prejudices in protein sequences. The oligopeptide preferences were used to help decide the significance of sequence homologies and to improve the more general methods for detecting protein coding regions within nucleotide sequences.