Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology |
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Authors: | JB Brown Tatsuya Akutsu |
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Institution: | (1) Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan |
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Abstract: | Background DNA repair is the general term for the collection of critical mechanisms which repair many forms of DNA damage such as methylation
or ionizing radiation. DNA repair has mainly been studied in experimental and clinical situations, and relatively few information-based
approaches to new extracting DNA repair knowledge exist. As a first step, automatic detection of DNA repair proteins in genomes
via informatics techniques is desirable; however, there are many forms of DNA repair and it is not a straightforward process
to identify and classify repair proteins with a single optimal method. We perform a study of the ability of homology and machine
learning-based methods to identify and classify DNA repair proteins, as well as scan vertebrate genomes for the presence of
novel repair proteins. Combinations of primary sequence polypeptide frequency, secondary structure, and homology information
are used as feature information for input to a Support Vector Machine (SVM). |
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