Sequence information signal processor for local and global string comparisons

Patent · Wed Jan 01 00:00:00 EST 1997

OSTI ID:870964

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

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1. Alta Loma, CA
2. San Dimas, CA
3. Culver City, CA
4. Pasadena, CA

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.

• Research Organization: California Institute of Technology (CalTech), Pasadena, CA (United States)
• DOE Contract Number: FG03-88ER60683
• Assignee: California Institute of Technology (Pasadena, CA)
• Patent Number(s): US 5632041
• OSTI ID: 870964
• Country of Publication: United States
• Language: English

Related Subjects

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
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