Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2002-02-22
2010-06-15
Zhou, Shubo (Joe) (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S020000, C703S011000, C435S006120
Reexamination Certificate
active
07739052
ABSTRACT:
Basis motifs are determined from an input sequence though an iterative technique that begins by creating small solid motifs and continues to create larger motifs that include “don't care” characters and that can include flexible portions. The small solid motifs, including don't care characters and flexible portions, are concatenated to create larger motifs. During each iteration, motifs are trimmed to remove redundant motifs and other motifs that do not meet certain criteria. The process is continued until no new motifs are determined. At this point, the basis set of motifs has been determined. The basis motifs are used to construct redundant motifs. The redundant motifs are formed by determining a number of sets for selected basis motifs. From these sets, unique intersection sets are determined. The redundant motifs are determined from the unique intersection sets and the basis motifs. This process continues, by selecting additional basis motifs.
REFERENCES:
patent: 6571230 (2003-05-01), Parida
patent: 2008/0294613 (2008-11-01), Iyer et al.
Myers et al. Science, vol. 287, pp. 2196-2204, Mar. 24, 2000.
SODA 2000. The Eleventh ACM-SIAM Symposium on Discrete Algorithms (SODA) was specifically held on Jan. 9-11, 2000. See “SODA 2000 program,” printed from the internet at <http://www.siam.org/meetings/da00/> on Jul. 7, 2008.
Parida et al., “Pattern Discovery on Character Sets and Real-Valued Data: Linear Bound on Irredundant Motifs and and Efficient Polynomial Time Algorithm,” Eleventh ACM-SIAM Symposium on Discrete Algorithms (SODA), 2000.
Parida et al., An Approximation Algorithm for Alignment of Multiple Sequences using Motif Discovery, Journal of Combinatorial Optimization 3, 247-275, 1999.
International Business Machines - Corporation
Ryan & Mason & Lewis, LLP
Zhou Shubo (Joe)
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