Methods for selecting nucleic acid probes

Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical

Reexamination Certificate

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

C702S020000, C435S006120, C707S793000, C536S023100

Reexamination Certificate

active

07117095

ABSTRACT:
Methods and computer software products are provided for selecting nucleic acid probes. In one embodiment, dynamic programming is employed to select a set of k probes from n probes so that the selected probes have a maximum aggregate adjusted quality score.

REFERENCES:
patent: 5571639 (1996-11-01), Hubbell et al.
patent: 5593839 (1997-01-01), Hubbell et al.
patent: 5800992 (1998-09-01), Fodor et al.
patent: 5837832 (1998-11-01), Chee et al.
patent: 5856101 (1999-01-01), Hubbell et al.
patent: 5862242 (1999-01-01), Takewa et al.
patent: 5871928 (1999-02-01), Fodor et al.
patent: 5959098 (1999-09-01), Goldberg et al.
patent: 6013449 (2000-01-01), Hacia et al.
patent: 6027880 (2000-02-01), Cronin et al.
patent: 6027884 (2000-02-01), Lane et al.
patent: 6040138 (2000-03-01), Lockhart et al.
patent: 6040183 (2000-03-01), Ferrari et al.
patent: 6130046 (2000-10-01), Hubbell et al.
patent: 6153743 (2000-11-01), Hubbell et al.
patent: 6188783 (2001-02-01), Balaban et al.
patent: 6251588 (2001-06-01), Shannon et al.
patent: 6307042 (2001-10-01), Goldberg et al.
patent: 6309823 (2001-10-01), Cronin et al.
patent: 6340565 (2002-01-01), Oliner et al.
patent: 6458530 (2002-10-01), Morris et al.
patent: 6468744 (2002-10-01), Cronin et al.
patent: 6706875 (2004-03-01), Goldberg et al.
patent: 6746844 (2004-06-01), Oliner et al.
patent: 6826296 (2004-11-01), Balaban et al.
patent: 2002/0102564 (2002-08-01), Mittmann et al.
Mei, G. et al. Octamer-primed sequencing technology: development of primer identification software. Nucleic Acids Research (Apr. 1, 2000) vol. 28 No. 7 pp. e22 (i-ix).
Burke et al., “A Validated Method for Clustering EST and Full-Length cDNA Sequences”,Genome Research, vol. 9, 1999, pp. 1135-1142.
Chee et al., “Accessing Genetic Information with High-Density DNA Arrays”,Science, abstract, vol. 274, Jul. 1996, 14 pages.
Cronin et al., “Cystic Fibrosis Mutation Detection by Hybridization to Light-Generated DNA Probe Arrays”,Human Mutation, vol. 7, 1996, pp. 244-255.
de Saizieu et al., “Bacteria transcript imaging by hybridization of total RNA to oligonucleotide arrays”,Nature Biotechnology, vol. 16, No. 1, Jan. 1998, pp. 45-48.
Hacia et al., “Strategies of Mutational Analysis of the Large Multiexon ATM Gene Using High-Density Oligonucleotide Arrays”,Genome Research, vol. 8, Issue 12, Dec. 1998; pp. 1245-1258.
Hacia et al., “Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-color fluorescence analysis”,Nature Genetics, vol. 14, 1996, pp. 441-447.
Hacia et al., “New approaches to BRCA1 mutation detection”,Breast Disease, vol. 10, pp. 45-59.
Kozal et al., “Extensive polymorphisms observed in HIV-1 clade B protease gene using high density oligonucleotide arrays”,Nature Medicine, vol. 2, No. 7, Jul. 1996, pp. 753-759.
Lockhart et al., “Expression monitoring by hybridization to high-density oligonucleotide arrays”,Nature Biotechnology, vol. 14, Dec. 1996, pp. 1675-1680.
Lander “Array of Hope”,Nature-Geneticsvol. 21, 1999.
Searls, “Bioinformatics Tools for Whole Genomex”,Annu. Rev. Genom. Hum. Genetics, vol. 1, 2000, pp. 251-279.
Ramsay, “DNA chips: State-of-Art”,Nature Biotechnology, vol. 16, 1998, pp. 40-44.
Wodicka et al., “Genome-wide Expression Monitoring inSaccharomyces cerevisiae”, Nature Biotechnology, vol. 15, Dec. 1997, pp. 1359-1367.
U.S. Appl. No. 09/721,042, filed Nov. 21, 2000, Hunt.
U.S. Appl. No. 09/718,295, filed Nov. 21, 2000, Mei.
U.S. Appl. No. 08/767,892, filed Dec. 17, 1996, Hubbell, et al.
U.S. Appl. No. 09/567,548, filed May 5, 2000, Hubbel, et al.
U.S. Appl. No. 09/607,536, filed Jun. 29, 2000, Hubbell, et al.
U.S. Appl. No. 10/975,245, filed Oct. 27, 2004, Hubbell, et al.
U.S. Appl. No. 09/811,364, filed Mar. 16, 2001, Balaban, et al.
U.S. Appl. No. 10/925,393, filed Aug. 24, 2004, Balaban, et al.
U.S. Appl. No. 09/640,962, filed Aug. 16, 2000, Hubbell.
U.S. Appl. No. 10/627,271, filed Jul. 25, 2003, Hubbell.
U.S. Appl. No. 11/038,614, filed Jan. 18, 2005, Hubbell, et al.
U.S. Appl. No. 10/226,355, filed Aug. 23, 2002, Morris, et al.
U.S. Appl. No. 10/017,034, filed Dec. 14, 2001, Mei, et al.
U.S. Appl. No. 10/308,379, filed Dec. 2, 2002, Mei.
U.S. Appl. No. 10/914,937, filed Aug. 9, 2004, Mei, et al.
U.S. Appl. No. 10/782,614, filed Feb. 19, 2004, Bekiranov, et al.
Cheng, et al; NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis; Bioinformatics Applications note; vol. 20; No. 9, 2004; pp. 1462-1463.
Cho, et al; Genome-wide Mapping with Biallelic Markers in Arabidopsis Thaliana; Nature Genetics, vol. 23, Oct. 1999 pp. 203-207.
Di, et al; Dynamic Model Based Algorithms for Screening and Genotyping over 100K SNPs on Oligonucleotide Microarrays; Bioinformatics Advance Access; Jan. 18, 2005.
Hubbell, et al; Fidelity Probes for DNA Arrays; Proc Int Conf Intell Sys Biol. 1999 (abstract).
Liu, et al; Analysis of High Density Expression Microarrays with Signed-Rank Call Algorithms; Bioinformatics; vol. 18; No. 12; 2000; pp. 1593-1599.
Mei, et al; Probe Selection for High-Density Oligonucleotide Arrays; PNAS; Sep. 30, 2003; vol. 100; No. 20; pp. 11237-11242.
Wang: et al; Gene Structure-Based Splice Variant Deconvolution Using a Microarray Platform: Bioinformatics; vol. 19; Suppl. 1; 2003; pp. i315-i1322.
Wang, et al; Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome; Science; vol. 280; May 15, 1998; pp. 1077-1082.

LandOfFree

Say what you really think

Search LandOfFree.com for the USA inventors and patents. Rate them and share your experience with other people.

Rating

Methods for selecting nucleic acid probes does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Methods for selecting nucleic acid probes, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Methods for selecting nucleic acid probes will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFUS-PAI-O-3683687

  Search
All data on this website is collected from public sources. Our data reflects the most accurate information available at the time of publication.