Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2005-05-24
2005-05-24
Allen, Marianne P. (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S020000
Reexamination Certificate
active
06898530
ABSTRACT:
Systems for creating high-dimensional vectors representing sequence strings and biopolymer materials are provided. A first system for divides respective sequence strings into blocks of at least three units to create a vocabulary of blocks. A second system selects predefined domains of a plurality of items of biopolymer materials. A third system defines each item of biopolymer material in a data set of biopolymer materials as a surface using descriptors of at least one of structure and function. A fourth system compares information regarding each biopolymer material of a plurality of biopolymer materials to information regarding each other biopolymer material.
REFERENCES:
patent: 5047842 (1991-09-01), Bouman, Jr. et al.
patent: 5121337 (1992-06-01), Brown
patent: 5325298 (1994-06-01), Gallant
patent: 5361326 (1994-11-01), Aparicio, IV et al.
patent: 5446681 (1995-08-01), Gethner et al.
patent: 5506937 (1996-04-01), Ford et al.
patent: 5528735 (1996-06-01), Strasnick et al.
patent: 5546472 (1996-08-01), Levin
patent: 5555354 (1996-09-01), Strasnick et al.
patent: 5592599 (1997-01-01), Lindholm
patent: 5619709 (1997-04-01), Caid et al.
patent: 5623679 (1997-04-01), Rivette et al.
patent: 5623681 (1997-04-01), Rivette et al.
patent: 5625767 (1997-04-01), Bartell et al.
patent: 5659766 (1997-08-01), Saund et al.
patent: 5671381 (1997-09-01), Strasnick et al.
patent: 5675788 (1997-10-01), Husick et al.
patent: 5687364 (1997-11-01), Saund et al.
patent: 5692107 (1997-11-01), Simoudis et al.
patent: 5696963 (1997-12-01), Ahn
patent: 5699507 (1997-12-01), Goodnow, II et al.
patent: 5721903 (1998-02-01), Anand et al.
patent: 5721912 (1998-02-01), Stepczyk et al.
patent: 5732260 (1998-03-01), Nomiyama
patent: 5737591 (1998-04-01), Kaplan et al.
patent: 5751612 (1998-05-01), Donovan et al.
patent: 5767854 (1998-06-01), Anwar
patent: 5784544 (1998-07-01), Stevens
patent: 5787274 (1998-07-01), Agrawal et al.
patent: 5794178 (1998-08-01), Caid et al.
patent: 5819258 (1998-10-01), Vaithyanathan et al.
patent: 5838973 (1998-11-01), Carpenter-Smith et al.
patent: 5842206 (1998-11-01), Sotomayor
patent: 5857179 (1999-01-01), Vaithyanathan et al.
patent: 5857185 (1999-01-01), Yamaura
patent: 5861891 (1999-01-01), Becker
patent: 5864863 (1999-01-01), Burrows
patent: 5873076 (1999-02-01), Barr et al.
patent: 5907838 (1999-05-01), Miyasaka et al.
patent: 5913214 (1999-06-01), Madnick et al.
patent: 5918010 (1999-06-01), Appleman et al.
patent: 5926806 (1999-07-01), Marshall et al.
patent: 5926820 (1999-07-01), Agrawal et al.
patent: 5930784 (1999-07-01), Hendrickson
patent: 5930803 (1999-07-01), Becker et al.
patent: 5945982 (1999-08-01), Higashio et al.
patent: 5953006 (1999-09-01), Baker et al.
patent: 5953716 (1999-09-01), Madnick et al.
patent: 5963965 (1999-10-01), Vogel
patent: 5966139 (1999-10-01), Anupam et al.
patent: 5982370 (1999-11-01), Kamper
patent: 5986652 (1999-11-01), Medl et al.
patent: 5986673 (1999-11-01), Martz
patent: 5987470 (1999-11-01), Meyers et al.
patent: 5991714 (1999-11-01), Shaner
patent: 5999192 (1999-12-01), Selfridge et al.
patent: 5999937 (1999-12-01), Ellard
patent: 6012053 (2000-01-01), Pant et al.
patent: 6014661 (2000-01-01), Ahlberg et al.
patent: 6023694 (2000-02-01), Kouchi et al.
patent: 6026409 (2000-02-01), Blumenthal
patent: 6029176 (2000-02-01), Cannon
patent: 6032157 (2000-02-01), Tamano et al.
patent: 6034697 (2000-03-01), Becker
patent: 6035057 (2000-03-01), Hoffman
patent: 6038538 (2000-03-01), Agrawal et al.
patent: 6038561 (2000-03-01), Snyder et al.
patent: 6044366 (2000-03-01), Graffe et al.
patent: 6049806 (2000-04-01), Crecine
patent: 6058391 (2000-05-01), Gardner
patent: 6067542 (2000-05-01), Carino, Jr.
patent: 6073115 (2000-06-01), Marshall
patent: 6073138 (2000-06-01), de l'Etraz et al.
patent: 6078314 (2000-06-01), Ahn
patent: 6078914 (2000-06-01), Redfern
patent: 6081788 (2000-06-01), Appleman et al.
patent: 6081802 (2000-06-01), Atherton et al.
patent: 6085190 (2000-07-01), Sakata
patent: 6088032 (2000-07-01), Mackinlay
patent: 6092061 (2000-07-01), Choy
patent: 6094648 (2000-07-01), Aalbersberg
patent: 6094649 (2000-07-01), Bowen et al.
patent: 6098065 (2000-08-01), Skillen et al.
patent: 6100901 (2000-08-01), Mohda et al.
patent: 6101493 (2000-08-01), Marshall et al.
patent: 6108004 (2000-08-01), Medl
patent: 6108651 (2000-08-01), Guha
patent: 6108666 (2000-08-01), Floratos et al.
patent: 6111578 (2000-08-01), Tesler
patent: 6112194 (2000-08-01), Bigus
patent: 6112209 (2000-08-01), Gusack
patent: 6121969 (2000-09-01), Jain et al.
patent: 6122636 (2000-09-01), Malloy et al.
patent: 6128624 (2000-10-01), Papierniak et al.
patent: 6252597 (2001-06-01), Lokuge
patent: 6259451 (2001-07-01), Tesler
patent: 6289353 (2001-09-01), Hazlehurst et al.
patent: 6327574 (2001-12-01), Kramer et al.
patent: 6484168 (2002-11-01), Pennock et al.
patent: 6493709 (2002-12-01), Aiken
patent: 0 202 686 (1986-11-01), None
patent: 0 627 692 (1994-07-01), None
patent: 0 717 346 (1996-06-01), None
patent: WO9927495 (1999-06-01), None
Altschul et al. Basic Local Alignment Search Tool. 1990. Journal of Molecular Biology. vol. 215, pp. 403-410.*
Higgins, Desmond G., “Sequence ordinations: a multivariate analysis approach to analyzing large sequence data sets,”Comput. Appl. Biosc., vol. 8, 1992, pp. 15-22.
“Screening Cheminformatics Data”, visited at http://www.partek.com/chem/screen.html on Apr. 15, 1999, 2 pages.
“Variable Transformation”, visited at http://www.partek.com/chem/tx.html on Apr. 15, 1999, 1 page.
“Visualization of High Dimensional Data”, Visited at http://www.partek.com/chem/viz.html on Apr. 15, 1999, 3 page.
“Correlating Activities w/Structural Descriptors”, visited at http://www.partek.com/chem/cor.html on Apr. 15, 1999, 6 pages.
“Cluster Analysis of Cheminformatics Data”, visited at http://www.partek.com/chem/cla.html on Apr. 15, 1999, 2 pages.
Cleveland, William S.,Visualizing Data, Hobart Press, Summit, New Jersey, 1993, pp. 1-360.
Nielson, Gregory M. et al.,Scientific Visualization, IEEE Computer Society, 1997, pp. 1-577.
Hobohm, Uwe et al., “A Sequence Property Approach to Searching Protein Databases”,Journal of Molecular Biology, 1995, pp. 390-399.
van Heel, Martin, “A New Family to Powerful Multivariate Statistical Sequence Analysis Techniques”,Journal of Molecular Biology, 1991, pp. 877-887.
Becker, Richard A. et al., “Brushing Scatterplots”,Technometrics, May 1987, vol. 29, No. 2, pp. 127-142.
Agrafiotis, Dimitris K., “A New Method for Analyzing Protein Sequence Relatsionships Based on Sammon Maps”,Protein Science, vol. 6, 1997, pp. 287-293.
Eisen, Michael B. et al., “Cluster Analysis and Display of Genome-Wide Expression Patterns,”Proc. Nat'l Acad. Sci., USA, vol. 95, 1998, pp. 14863-14868.
“Silicon Graphics MineSet™, Supporting the Discovery Research Process,”MineSet for Discovery Research, Spring 1999, pp. 1-49.
“Spotfire Pro 4.0—Speeding Discovery”, visited at http://www.sportfire.com/of_2_1.htm on Jun. 17, 1999, 2 pages.
“Spotfire Pro—Offerings—Spotfire”, visited at http://www.spotfire.com/of on Jun. 17, 1999, 2 pages.
“Discovery Innovation—Spotfire”, visited at http://www.spotfire.com/di_1_1.htm. on Jun. 17, 1999, 1 page.
“Discovery Innovation—Spotfire”, visited at http://www.spotfire.com/di_1_1_4.htm on Jun. 17, 1999, 1 page.
“Downloads—Spotfire”, visited at http://www.spotfire.com/down_00.htm#2.1.2 on Jun. 17, 1999, 1 page.
“Offerings—Spotfire”, visited at http://www.spotfire.com/of_2_4.htm on Jun. 17, 1999, 1 page.
“Partners—Spotfire”, visited at http://www.spotfire.com/pa_4_0.htm on Jun. 17, 1999, 2 pages.
“Partners—Spotfire”, visited at http://www.spotfire.com/pa_4_2.htm on Jun. 17, 1999, 1 page.
“Cheminformatics Example”, visited at http://www.partek.com/chem/index,htm
Calapristi Augustin J.
Chen Guang
Miller Nancy E.
Monroe Philip J.
Saffer Jeffrey D.
Allen Marianne P.
Battelle (Memorial Institute)
Finnegan Henderson Farabow Garrett & Dunner L.L.P.
Linnik Konstantin M.
Mahatan Channing S.
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