29 Questions
What is the main focus of Section 6 in the text?
Development of logical structure in the Central Control Unit
What is the purpose of the L-mer generator in the organization described in the text?
Generating patterns of specified size starting from 0
In the bit parallel organization shown in Fig. 1, what does each slice in the AMAP correspond to?
Specific DNA sequence
What is the requirement for S and the number of PEs in each slice according to the text?
$S ext{ should be} extgreater T ext{ and Number of PEs should be} extgreater N-L+1$
What type of operations are performed by each processing element (PE) in the AMAP?
Input loading, simple comparisons in parallel, match scoring
What does the WR array hold according to the text?
Generated windows each with a specific WR
Which of the following is the main focus of the paper by Fortune and Wyllie?
Parallelism in Random Access Machines
What is the primary contribution of the paper by Jon A. Webb?
Steps towards architecture-independent image processing
What is the main topic of the paper by N. El-Nadi, G. Aly, and H.M. Faheem?
AMAP for Typecasting
Which of the following papers discusses the theory and practice of parallel computing?
Michael J. Quinn's book on Parallel Computing Theory and Practice
Which of the following papers discusses approaches to finding patterns in DNA sequences?
E. Eskin and P. Pevzner's paper on finding composite regulatory patterns in DNA sequences
What is TCOMP in the context of performance evaluation?
The time needed to perform the comparisons of the WR and L-mer
Which factor contributed to the achieved speedup when comparing the AMAP run time with Matlab run time?
TCOMP
In the context provided, what does TSLICE represent?
The time needed to load all the windows of the DNA sequences into the slices
Based on Table 1, which problem size had the shortest TEXEC in seconds?
(9,2)
What is the main advantage of the proposed system in comparison to sequential implementations?
Ability to achieve better run time
Which processor was used for the Matlab run time according to the text?
AMD 5500 X2+ processor
What is the purpose of the special parallel adder in the calculation of Total L-mer?
To facilitate the comparison of generated L-mer with all windows concurrently
What does the operation of the PE involve according to the text?
Comparing windows with the generated L-mer
How is the total number of L-mer occurrences calculated?
By calculating the matching score of the L-mer in all slices
What occurs during the comparison process in the PE operation?
Concurrently comparing all windows with the generated L-mer
What is the role of AMAP Architecture described in the text?
To facilitate parallel comparisons between L-mer and all windows
What is the primary function of All PEs mentioned in the text?
Comparing windows with the generated L-mer
What is a key feature of the system's design for DNA search applications?
Complexity independent of motif length and number of sequences
Which publication describes an exact algorithm for planted motif challenge problems?
S.Rajasekaran et al., Asia-Pacific Bioinformatics Conference 2005
What type of architecture is the system considered a step towards?
Special-purpose parallel architecture
In which field does the publication by Siggelkow and Burkhardt focus on?
Image retrieval based on local invariant features
Which publication discusses the discovery and analysis of DNA and protein motifs?
T.L.Bailey et al., Nucleic Acid Research 2006
What characteristic allows the system to be suitable for a wide range of DNA search applications?
Independence from motif length and number of sequences
This quiz covers the development of the logical structure of the Central Control Unit, system operation summary, performance evaluation, and concluding remarks. It discusses the bit parallel organization with input unit, output unit, associative memory array processor (AMAP), and central control unit.
Make Your Own Quizzes and Flashcards
Convert your notes into interactive study material.
Get started for free
