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Genomics Inform > Volume 3(2); 2005 > Article
Classification of Peroxiredoxin Subfamilies Using Regular Expressions.
Jae Kyung Chon, Jongkeun Choi, Sang Soo Kim, Whanchul Shin
1Department of Chemistry, Seoul National University, Seoul 151-742, Korea.
2Department of Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea.
3Department of Bioinformatics, Soongsil University, Seoul 156-743, Korea. sskimb@ssu.ac.kr
Abstract
Peroxiredoxins (Prx's) are a superfamily of peroxidases that are ubiquitous in all super-kingdoms. Previous biochemical and structural studies have suggested that Prx's could be divided into five subfamilies (1-Cys, Typical 2-Cys, Atypical 2-Cys C-, L- and R- types). In this work, we have developed a set of regular expression patterns describing subfamily-specific spatial constraints of the key catalytic residues. Using these patterns, 1,016 Prx's available in public databases were classified into the five subfamilies. Our method performed well for most of the types except for Atypical 2 Cys R type.
Keywords: peroxiredoxin; regular expression; subfamily classification


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