A method for matching sequences of protein secondary structures

• Autorzy: Wieczorek D. , Małysiak-Mrozek B. , Kozielski S. , Mrozek D.
• Języki publikacji: EN

Abstrakty

EN

Alignment of specific regions of two biological molecules is a basic method for determination how similar these two molecules are. There are several methods of optimal alignment that were developed through many years. However, they are dedicated for nucleotide sequences of DNA⁄RNA or amino acid sequences of proteins. Since the construction of proteins can also be analyzed at the level of secondary structure (and higher), we need a comparative method, which would allow us to determine the similarity between biological particles at this level and express it through the appropriate similarity measure. For this reason, we have modified an existing Smith–Waterman method towards matching sequences of secondary structures elements (SSEs). In the paper, we present our modification to the method. We also describe how we find several alternative and equally optimal alignment paths on the basis of the characteristics of compared sequences. Presented alignment method is used in the PSS–SQL language, which allows searching a database in order to find proteins having secondary structures similar to the structural pattern specified by a user.

Słowa kluczowe

EN

proteins; secondary structure; protein similarity; alignment

PL

proteiny; struktura drugorzędowa; podobieństwa białek; wyrównanie

• Wydawca: University of Silesia, Institute of Informatics, Computer Systems Department
• Czasopismo: Journal of Medical Informatics & Technologies
• Rocznik: 2010
• Tom: Vol. 16
• Strony: 133--137
• Opis fizyczny: Bibliogr. 17 poz., rys.

Twórcy

autor

Wieczorek D.

• Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland

autor

Małysiak-Mrozek B.

autor

Kozielski S.

autor

Mrozek D.

Bibliografia

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