18 Questions
What elements are included in the bit parallel organization used in the system?
Input unit, output unit, associative memory array processor (AMAP), central control unit
What does the L-mer generator in the input unit consist of?
A simple counter capable of generating patterns of size 2L bits
What does the associative memory array processor (AMAP) consist of?
A set of slices, each responsible for a specific DNA sequence
What is the main function of each processing element (PE) in the system?
Capable of processing data, including input loading, simple comparisons in parallel, and match scoring
What is the role of the control unit in the system?
To develop the logical structure of the processing Central Control Unit element
How is data processed during the motif finding problem in the system?
Each slice provides the match count for the occurrence of the generated L-mer in a specific DNA sequence
What is the responsibility of the n-bit SS in the DNA sequence loading process?
Selecting a specific slice
How does the PE determine an exact match between the L-mer and the window of the sequence?
Using XNOR gates to compare corresponding positions
How is the score of the exact match calculated by the PE?
By adding the contents of two memory blocks
What determines if the L-mer is matched with the window according to the PE?
Score of the exact match ≥ (L-M)
What does the PE use to calculate the total number of occurrences of the L-mer in a DNA sequence for a given slice?
MSU of the slice
How does the PE determine the output F?
As in (1)
What is the main concern when solving the motif finding problem?
TSEQ
What does TDISP refer to in the context of processing DNA sequences?
The time needed to display the results
What is the purpose of implementing parallel processing architectures in this context?
To perform comparisons in parallel
What does TLOAD depend on in the context of DNA sequence processing?
Number of windows that could be generated
What are some of the stages implemented in AMAP for processing different problem sizes?
L-mer generator counters, L-mer windows registers, parallel comparison
What is the role of the TSLICE element in the processing element of the system?
Calculate the occurrences of the L-mer into the slice
Explore the development of the logical structure of the processing Central Control Unit, summary of system operation, performance evaluation, and concluding remarks. Learn about the bit parallel organization including input unit, output unit, associative memory array processor AMAP, and central control unit.
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