Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2006-08-01
2006-08-01
Borin, Michael (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S020000
Reexamination Certificate
active
07085651
ABSTRACT:
An object of the present invention is to perform the clustering and assembling of nucleic acid base sequences at a high speed. Partial sequences102are extracted from each input sequence101and entered into a fixed-length partial sequence table103. In the case where a sequence overlapping with a consensus sequence104is searched while making reference to the fixed-length partial sequence table103and consequently a partial sequence102, which exactly matches with a sequence defined by a fixed length window105scanning along the consensus sequence, is found to be present, whether the whole input sequence can be assembled or not is determined by comparing the sequences. If it is possible to assemble the sequences, they are assembled into a consensus sequence and also joined into the same cluster. The clustering and assembling are performed by repeatedly processing this procedure based on greedy method until no unprocessed input nucleic acid base sequence is left.
REFERENCES:
Xiaoqiu Huang and Anup Madan, “CAP3: a DNA Sequence Assembly Program”, Genome Research (1999) pp. 868-877.
Zheng Zhang, Scott Schwartz, Lukas Wagner and Webb Miller, “A greedy Algorithm for Aligning DNA Sequences”, Journal of Computational Biology, vol. 7, No. 1/2 , 2000, pp. 203-214.
Stephen F. Altshcul, Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller and David J. Lipman, “Gapped BLAST and PSI-BLAST: a New Generation of Protein Database Search Programs”, Nucleic Acids Research, 1997, vol. 25, No. 17, pp. 3389-3402.
Nishikawa Tetsuo
Yasuda Tomohiro
A. Marquez, Esq. Juan Carlos
Borin Michael
Fisher Esq. Stanley P.
Hitachi , Ltd.
Reed Smith LLP
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