Sequence information signal processor for local and global string comparisons

Peterson, John C; Chow, Edward T; Waterman, Michael S; Hunkapillar, Timothy J

Advanced Search OptionsAdvanced Search queries use a traditional Term Search. For more info, see our FAQ.

All Fields:

Patent Title:

Abstract:

Assignee:

Inventor(s):

Patent Number:

Patent Classification (CPC):

All Classifications
A - human necessities
A01 - agriculture
A21 - baking
A22 - butchering
A23 - foods or foodstuffs
A24 - tobacco
A41 - wearing apparel
A42 - headwear
A43 - footwear
A44 - haberdashery
A45 - hand or travelling articles
A46 - brushware
A47 - furniture
A61 - medical or veterinary science
A62 - life-saving
A63 - sports
A99 - subject matter not otherwise provided for in this section
B - performing operations
B01 - physical or chemical processes or apparatus in general
B02 - crushing, pulverising, or disintegrating
B03 - separation of solid materials using liquids or using pneumatic tables or jigs
B04 - centrifugal apparatus or machines for carrying-out physical or chemical processes
B05 - spraying or atomising in general
B06 - generating or transmitting mechanical vibrations in general
B07 - separating solids from solids
B08 - cleaning
B09 - disposal of solid waste
B21 - mechanical metal-working without essentially removing material
B22 - casting
B23 - machine tools
B24 - grinding
B25 - hand tools
B26 - hand cutting tools
B27 - working or preserving wood or similar material
B28 - working cement, clay, or stone
B29 - working of plastics
B30 - presses
B31 - making articles of paper, cardboard or material worked in a manner analogous to paper
B32 - layered products
B33 - additive manufacturing technology
B41 - printing
B42 - bookbinding
B43 - writing or drawing implements
B44 - decorative arts
B60 - vehicles in general
B61 - railways
B62 - land vehicles for travelling otherwise than on rails
B63 - ships or other waterborne vessels
B64 - aircraft
B65 - conveying
B66 - hoisting
B67 - opening, closing {or cleaning} bottles, jars or similar containers
B68 - saddlery
B81 - microstructural technology
B82 - nanotechnology
B99 - subject matter not otherwise provided for in this section
C - chemistry
C01 - inorganic chemistry
C02 - treatment of water, waste water, sewage, or sludge
C03 - glass
C04 - cements
C05 - fertilisers
C06 - explosives
C07 - organic chemistry
C08 - organic macromolecular compounds
C09 - dyes
C10 - petroleum, gas or coke industries
C11 - animal or vegetable oils, fats, fatty substances or waxes
C12 - biochemistry
C13 - sugar industry
C14 - skins
C21 - metallurgy of iron
C22 - metallurgy
C23 - coating metallic material
C25 - electrolytic or electrophoretic processes
C30 - crystal growth
C40 - combinatorial technology
C99 - subject matter not otherwise provided for in this section
D - textiles
D01 - natural or man-made threads or fibres
D02 - yarns
D03 - weaving
D04 - braiding
D05 - sewing
D06 - treatment of textiles or the like
D07 - ropes
D10 - indexing scheme associated with sublasses of section d, relating to textiles
D21 - paper-making
D99 - subject matter not otherwise provided for in this section
E - fixed constructions
E01 - construction of roads, railways, or bridges
E02 - hydraulic engineering
E03 - water supply
E04 - building
E05 - locks
E06 - doors, windows, shutters, or roller blinds in general
E21 - earth drilling
E99 - subject matter not otherwise provided for in this section
F - mechanical engineering
F01 - machines or engines in general
F02 - combustion engines
F03 - machines or engines for liquids
F04 - positive - displacement machines for liquids
F05 - indexing schemes relating to engines or pumps in various subclasses of classes f01-f04
F15 - fluid-pressure actuators
F16 - engineering elements and units
F17 - storing or distributing gases or liquids
F21 - lighting
F22 - steam generation
F23 - combustion apparatus
F24 - heating
F25 - refrigeration or cooling
F26 - drying
F27 - furnaces
F28 - heat exchange in general
F41 - weapons
F42 - ammunition
F99 - subject matter not otherwise provided for in this section
G - physics
G01 - measuring
G02 - optics
G03 - photography
G04 - horology
G05 - controlling
G06 - computing
G07 - checking-devices
G08 - signalling
G09 - education
G10 - musical instruments
G11 - information storage
G12 - instrument details
G16 - information and communication technology [ict] specially adapted for specific application fields
G21 - nuclear physics
G99 - subject matter not otherwise provided for in this section
H - electricity
H01 - basic electric elements
H02 - generation
H03 - basic electronic circuitry
H04 - electric communication technique
H05 - electric techniques not otherwise provided for
H99 - subject matter not otherwise provided for in this section
Y - new / cross sectional technologies
Y02 - technologies or applications for mitigation or adaptation against climate change
Y04 - information or communication technologies having an impact on other technology areas
Y10 - technical subjects covered by former uspc

More Options ...

Title: Sequence information signal processor for local and global string comparisons

Abstract

A sequence information signal processing integrated circuit chip designed to perform high speed calculation of a dynamic programming algorithm based upon the algorithm defined by Waterman and Smith. The signal processing chip of the present invention is designed to be a building block of a linear systolic array, the performance of which can be increased by connecting additional sequence information signal processing chips to the array. The chip provides a high speed, low cost linear array processor that can locate highly similar global sequences or segments thereof such as contiguous subsequences from two different DNA or protein sequences. The chip is implemented in a preferred embodiment using CMOS VLSI technology to provide the equivalent of about 400,000 transistors or 100,000 gates. Each chip provides 16 processing elements, and is designed to provide 16 bit, two's compliment operation for maximum score precision of between -32,768 and +32,767. It is designed to provide a comparison between sequences as long as 4,194,304 elements without external software and between sequences of unlimited numbers of elements with the aid of external software. Each sequence can be assigned different deletion and insertion weight functions. Each processor is provided with a similarity measure device which is independentlymore » « less

Inventors:

Peterson, John C ^[1]; Chow, Edward T ^[2]; Waterman, Michael S ^[3]; Hunkapillar, Timothy J ^[4]

Alta Loma, CA
San Dimas, CA
Culver City, CA
Pasadena, CA

Issue Date:: 1997-01-01

Research Org.:: California Institute of Technology (CalTech), Pasadena, CA (United States)

OSTI Identifier:: 870964

Patent Number(s):: 5632041

Assignee:: California Institute of Technology (Pasadena, CA)

Patent Classifications (CPCs):: G - PHYSICS G06 - COMPUTING G06F - ELECTRIC DIGITAL DATA PROCESSING

Show more

G - PHYSICS G06 - COMPUTING G06F - ELECTRIC DIGITAL DATA PROCESSING
G06F11/2028 - {eliminating a faulty processor or activating a spare}
G06F11/2035 - {without idle spare hardware}
G06F11/2043 - {where the redundant components share a common memory address space}
G06F11/2051 - {in regular structures}
G06F11/2236 - {to test CPU or processors}
G06F17/10 - Complex mathematical operations {
G06F2201/83 - the solution involving signatures
G06F7/02 - Comparing digital values

Show less

DOE Contract Number:: FG03-88ER60683

Resource Type:: Patent

Country of Publication:: United States

Language:: English

Subject:: sequence; information; signal; processor; local; global; string; comparisons; processing; integrated; circuit; chip; designed; perform; speed; calculation; dynamic; programming; algorithm; based; defined; waterman; smith; building; block; linear; systolic; array; performance; increased; connecting; additional; chips; provides; cost; locate; highly; similar; sequences; segments; contiguous; subsequences; dna; protein; implemented; preferred; embodiment; cmos; vlsi; technology; provide; equivalent; 400; 000; transistors; 100; gates; 16; elements; bit; compliment; operation; maximum; score; precision; -32; 768; 32; 767; comparison; 194; 304; external; software; unlimited; assigned; deletion; insertion; weight; functions; provided; similarity; measure; device; independently; variable; contribute; value; information signal; linear array; signal processor; signal processing; preferred embodiment; integrated circuit; circuit chip; chip design; sequence information; maximum value; signal process; dynamic programming; independently variable; highly similar; algorithm based; /712/

Citation Formats


                    Peterson, John C, Chow, Edward T, Waterman, Michael S, and Hunkapillar, Timothy J. Sequence information signal processor for local and global string comparisons.  United States: N. p., 1997. 
        Web.

Copy to clipboard


                    Peterson, John C, Chow, Edward T, Waterman, Michael S, & Hunkapillar, Timothy J. Sequence information signal processor for local and global string comparisons.  United States.

Copy to clipboard


                    Peterson, John C, Chow, Edward T, Waterman, Michael S, and Hunkapillar, Timothy J. Wed .  
        "Sequence information signal processor for local and global string comparisons".  United States.  https://www.osti.gov/servlets/purl/870964.

Copy to clipboard


                    
@article{osti_870964,

  title        = {Sequence information signal processor for local and global string comparisons},

  author       = {Peterson, John C and Chow, Edward T and Waterman, Michael S and Hunkapillar, Timothy J},

  abstractNote = {A sequence information signal processing integrated circuit chip designed to perform high speed calculation of a dynamic programming algorithm based upon the algorithm defined by Waterman and Smith. The signal processing chip of the present invention is designed to be a building block of a linear systolic array, the performance of which can be increased by connecting additional sequence information signal processing chips to the array. The chip provides a high speed, low cost linear array processor that can locate highly similar global sequences or segments thereof such as contiguous subsequences from two different DNA or protein sequences. The chip is implemented in a preferred embodiment using CMOS VLSI technology to provide the equivalent of about 400,000 transistors or 100,000 gates. Each chip provides 16 processing elements, and is designed to provide 16 bit, two's compliment operation for maximum score precision of between -32,768 and +32,767. It is designed to provide a comparison between sequences as long as 4,194,304 elements without external software and between sequences of unlimited numbers of elements with the aid of external software. Each sequence can be assigned different deletion and insertion weight functions. Each processor is provided with a similarity measure device which is independently variable. Thus, each processor can contribute to maximum value score calculation using a different similarity measure.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {1997},

  month        = {1}

}

Copy to clipboard

Patent:

Save / Share:

Export Metadata

Save to My Library

Works referenced in this record:

Computational approaches to discovering semantics in molecular biology
journal, July 1989

Lipton, R. J.; Marr, T. G.; Welsh, J. D.
Proceedings of the IEEE, Vol. 77, Issue 7
https://doi.org/10.1109/5.30755

Design of special-purpose VLSI chips: Example and opinions
conference, January 1980

Foster, M. J.; Kung, H. T.
Proceedings of the 7th annual symposium on Computer Architecture - ISCA '80
https://doi.org/10.1145/800053.801938

Supercomputing in molecular biology: applications to sequence analysis
journal, December 1988

Maizel, J. V.
IEEE Engineering in Medicine and Biology Magazine, Vol. 7, Issue 4
https://doi.org/10.1109/51.20377

A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons
journal, October 1987

Waterman, Michael S.; Eggert, Mark
Journal of Molecular Biology, Vol. 197, Issue 4
https://doi.org/10.1016/0022-2836(87)90478-5

On high-speed computing with a programmable linear array
journal, September 1990

Lee, Peizong; Kedem, Zvi M.
The Journal of Supercomputing, Vol. 4, Issue 3
https://doi.org/10.1007/BF00127833

Similar Records in DOE Patents and OSTI.GOV collections:

Sequence information signal processor

Patent Peterson, John C [Alta Loma, CA]; Chow, Edward T [San Dimas, CA]; Waterman, Michael S [Culver City, CA]; ...

An electronic circuit is used to compare two sequences, such as genetic sequences, to determine which alignment of the sequences produces the greatest similarity. The circuit includes a linear array of series-connected processors, each of which stores a single element from one of the sequences and compares that element with each successive element in the other sequence. For each comparison, the processor generates a scoring parameter that indicates which segment ending at those two elements produces the greatest degree of similarity between the sequences. The processor uses the scoring parameter to generate a similar scoring parameter for a comparison betweenmore » « less
Full Text Available
Multiple core computer processor with globally-accessible local memories

Patent Shalf, John; Donofrio, David; Oliker, Leonid

A multi-core computer processor including a plurality of processor cores interconnected in a Network-on-Chip (NoC) architecture, a plurality of caches, each of the plurality of caches being associated with one and only one of the plurality of processor cores, and a plurality of memories, each of the plurality of memories being associated with a different set of at least one of the plurality of processor cores and each of the plurality of memories being configured to be visible in a global memory address space such that the plurality of memories are visible to two or more of the plurality ofmore » processor cores. « less
Full Text Available
Multiple core computer processor with globally-accessible local memories

Patent Shalf, John; Donofrio, David; Oliker, Leonid

A multi-core computer processor including a plurality of processor cores interconnected in a Network-on-Chip (NoC) architecture, a plurality of caches, each of the plurality of caches being associated with one and only one of the plurality of processor cores, and a plurality of memories, each of the plurality of memories being associated with a different set of at least one of the plurality of processor cores and each of the plurality of memories being configured to be visible in a global memory address space such that the plurality of memories are visible to two or more of the plurality ofmore » processor cores. « less
Full Text Available
Method and apparatus for combinatorial logic signal processor in a digitally based high speed x-ray spectrometer

Patent Warburton, William K [1300 Mills St., Menlo Park, CA 94025]; Zhou, Zhiquing [Carl; Fremont, CA]

A high speed, digitally based, signal processing system which accepts a digitized input signal and detects the presence of step-like pulses in the this data stream, extracts filtered estimates of their amplitudes, inspects for pulse pileup, and records input pulse rates and system livetime. The system has two parallel processing channels: a slow channel, which filters the data stream with a long time constant trapezoidal filter for good energy resolution; and a fast channel which filters the data stream with a short time constant trapezoidal filter, detects pulses, inspects for pileups, and captures peak values from the slow channel formore » « less
Full Text Available
Global synchronization of parallel processors using clock pulse width modulation

Patent Chen, Dong; Ellavsky, Matthew R.; Franke, Ross L.; ...

A circuit generates a global clock signal with a pulse width modification to synchronize processors in a parallel computing system. The circuit may include a hardware module and a clock splitter. The hardware module may generate a clock signal and performs a pulse width modification on the clock signal. The pulse width modification changes a pulse width within a clock period in the clock signal. The clock splitter may distribute the pulse width modified clock signal to a plurality of processors in the parallel computing system.
Full Text Available

Similar Records

Title: Sequence information signal processor for local and global string comparisons

Abstract

Citation Formats

Computational approaches to discovering semantics in molecular biology journal, July 1989

Design of special-purpose VLSI chips: Example and opinions conference, January 1980

Supercomputing in molecular biology: applications to sequence analysis journal, December 1988

A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons journal, October 1987

On high-speed computing with a programmable linear array journal, September 1990

Computational approaches to discovering semantics in molecular biology
journal, July 1989

Design of special-purpose VLSI chips: Example and opinions
conference, January 1980

Supercomputing in molecular biology: applications to sequence analysis
journal, December 1988

A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons
journal, October 1987

On high-speed computing with a programmable linear array
journal, September 1990