Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2003-04-29
2011-10-04
Negin, Russell S (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S022000, C435S006120
Reexamination Certificate
active
08032305
ABSTRACT:
A base sequence cluster generating system, method, and program product for performing cluster generation is provided. This is accomplished utilizing a computer system having a database containing base sequences which receives a query sequence. The computer uses spliced base sequences as a query sequence to generate a first cluster including base sequences that are likely to constitute a spliced pair with the query sequence. Spliced alignment is applied to the generated first cluster to generate a second cluster including spliced pairs. The generated second cluster is returned to the requester.
REFERENCES:
patent: 6893840 (2005-05-01), Thudium et al.
patent: 2314447 (2001-01-01), None
Zhang et al. Fission yeast gene structure and recognition. Nucleic Acids Research, 1994, vol. 22, pp. 1750-1759.
Florea et al. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Research, 1998, vol. 8, pp. 967-974.
Lewin B. Genes V: New York: Oxford University Press, 1994, pp. 150 and164.
Drmanac et al. Sequencing of megabase plus DNA by hybridization: theory of the method. Genomics, vol. 4, 1989, pp. 114-128.
Saris et al. cDNA sequence and tissue distribution of the mRNA for bovine and murine p11, the S100-related light chain of the protein-tyrosine kinase substrate p36 (Calpactin I). The Journal of Biological Chemistry. vol. 262, 1987, pp. 10663-10671.
Navarro et al. A new indexing method for approximate string matching. LNCS, 1999, vol. 1645, pp. 163-185.
Tanaka et al. Autonomous distributed genome database and its application to mouse cDNA and human genome sequence matching. Genome Informatics, vol. 11, pp. 378-379.
Jonathan Usuka, Wei Zhu and Volker Brendel, “Optimal Spliced Alignment of Homologous cDNA to a Genomic DNA Template,” Bioinformatics, vol. 16, No. 3, 2000, pp. 203-211.
G. Navarro and R. Baeza-Yates, “A New Indexing Method for Approximate String Matching,” Proc. CPM99, LNCS 1645, pp. 163-185, 1999.
R. Mott, “EST—GENOME: A Program to Align Spliced DNA Sequences,” CABIOS, vol. 13, No. 4, 1997, pp. 477-478.
J. Kawai et al., “Functional annotation of a full-length mouse cDNA collection,” Nature, vol. 409, pp. 685-690, 2001.
Gonzalo Navarro, “A Guided Tour to Approximate String Matching,” ACM Computer Surveys, vol. 33, No. 1, Mar. 2001, pp. 31-88.
Tetsuo Shibuya et al., “Accurate cDNA Clustering Algorithm Based on Spliced Sequence Alignment,” Technical Report of IEICE, COMP2002-11 (May 2002).
Tetsuo Shibuya et al., “Efficient filtering methods for clustering cDNAs with spliced sequence alignment,” Bioinformatics, vol. 20, No. 1, 2004, pp. 29-39.
International Business Machines - Corporation
Karen Canaan CanaanLaw, P.C.
Negin Russell S
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