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2 Journal of Medical Informatics & Technologies

2 2010

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A method for matching sequences of protein secondary structures

Wieczorek D., Małysiak-Mrozek B., Kozielski S., Mrozek D.

Journal of Medical Informatics & Technologies

2010

Vol. 16

133--137

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.

A declarative query language for protein secondary structures

Wieczorek D., Małysiak-Mrozek B., Kozielski S., Mrozek D.

Journal of Medical Informatics & Technologies

2010

Vol. 16

139--148

Searching proteins on their secondary structures provides a rough and fast method of identification of molecules having a similar fold. Since existing database management systems do not offer integrated exploration methods for querying protein structures, the structural similarity searching is usually performed by external tools. This often lengthens the processing time and requires additional processing steps, like adaptation of input and output data formats. In the paper, we present the extended SQL language, which allows searching a database in order to find proteins having secondary structures similar to the structural pattern specified by a user. Presented query language is integrated with the relational database management system and it simplifies the manipulation of biological data.