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2004 IEEE Computational Systems Bioinformatics Conference (CSB'04)
PRUNER: Algorithms for Finding Monad Patterns in DNA Sequences
Stanford, California
August 16-August 19
ISBN: 0-7695-2194-0
Ravi VijayaSatya, University of Central Florida
Amar Mukherjee, University of Central Florida
We present new algorithms for discovering monad patterns in DNA sequences. Monad patterns are of the form (l, d)-k, where l is the length of the pattern, d is the maximum number of mismatches allowed, and k is the minimum number of times the pattern is repeated in the given sample. The time-complexity of some of the best known algorithms to date is O(nt^2 l^d \left| \sum \right|^d ), where t is the number of input sequences, and n is the length of each input sequence. The first algorithm that we present takes O(n^2 t^2 l^{{d \mathord{\left/ {\vphantom {d 2}} \right. \kern-\nulldelimiterspace} 2}}\left| \Sigma \right|^{{d \mathord{\left/ {\vphantom {d 2}} \right. \kern-\nulldelimiterspace} 2}} ) and space 0(ntl^{{d \mathord{\left/ {\vphantom {d 2}} \right. \kern-\nulldelimiterspace} 2}} \left| \Sigma \right|^{{d \mathord{\left/ {\vphantom {d 2}} \right. \kern-\nulldelimiterspace} 2}} ), and the second algorithm takes 0(n^3 t^3 l^{{d \mathord{\left/ {\vphantom {d 2}} \right. \kern-\nulldelimiterspace} 2}} \left| \Sigma \right|^{{d \mathord{\left/ {\vphantom {d 2}} \right. \kern-\nulldelimiterspace} 2}} ) time using 0(l^{{d \mathord{\left/ {\vphantom {d 2}} \right. \kern-\nulldelimiterspace} 2}} \left| \Sigma \right|^{{d \mathord{\left/ {\vphantom {d 2}} \right. \kern-\nulldelimiterspace} 2}} ) space. In practice, our algorithms have much better performance provided the d/l ratio is small.
Index Terms:
Pattern discovery, regulatory patterns, k-mismatch patterns
Citation:
Ravi VijayaSatya, Amar Mukherjee, "PRUNER: Algorithms for Finding Monad Patterns in DNA Sequences," csb, pp.662-665, 2004 IEEE Computational Systems Bioinformatics Conference (CSB'04), 2004
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