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Author Srinivasan, S. ♦ Kamakoti, V. ♦ Bhattacharya, A.
Source ACM Digital Library
Content type Text
Publisher Association for Computing Machinery (ACM)
File Format PDF
Copyright Year ©2013
Language English
Subject Domain (in DDC) Computer science, information & general works ♦ Data processing & computer science
Subject Keyword DNA ♦ Embedding of microarrays ♦ Microarrays ♦ Placement of microarrays ♦ Synthesis of microarrays
Abstract DNA microarrays are used extensively for biochemical analysis that includes genomics and drug discovery. This increased usage demands large microarrays, thus complicating their computer aided design (CAD) and manufacturing methodologies. One such time-consuming design problem is to minimize the border length of masks used during the manufacture of microarrays. From the manufacturing point of view the border length of masks is one of the crucial parameters determining the reliability of the microarray. This article presents a novel algorithm for synthesis (placement and embedding) of microarrays, which consumes significantly less time than the best algorithm reported in the literature, while maintaining the quality (border length of masks) of the result. The proposed technique uses only a part of each probe to decide on the placement and the remaining parts for deciding on the embedding sequence. This is in contrast to the earlier methods that considered the entire probe for both placement and embedding. The second novelty of the proposed technique is the preclassification (prior to placement and embedding) of probes based on their prefixes. This decreases the complexity of the problem of deciding the next probe to be placed from that involving computation of Hamming distance between all probes (as used in earlier approaches) to the one involving searching of nonempty cells on a constant size grid array. The proposed algorithm is 43× faster than the best reported in the literature for the case of synthesizing a microarray with 250,000 probes and further exhibits linear behavior in terms of computation time for larger microarrays.
ISSN 15504832
Age Range 18 to 22 years ♦ above 22 year
Educational Use Research
Education Level UG and PG
Learning Resource Type Article
Publisher Date 2013-02-01
Publisher Place New York
e-ISSN 15504840
Journal ACM Journal on Emerging Technologies in Computing Systems (JETC)
Volume Number 9
Issue Number 1
Page Count 17
Starting Page 1
Ending Page 17


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Source: ACM Digital Library