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KMID : 0380020110260020131
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Korean Journal of Biotechnology and Bioengineering
2011 Volume.26 No. 2 p.131 ~ p.138
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Bioinformatics Approach to Direct Target Prediction for RNAi Function and Non-specific Cosuppression in Caenorhabditis elegans
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Kim Tae-Ho
Kim Eui-Yong
Joo Hyun
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Abstract
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Some computational approaches are needed for clarifying RNAi sequences, because it takes much time and endeavor that almost of RNAi sequences are verified by experimental data. Incorrectness of RNAi mechanism and other unaware factors in organism system are frequently faced with questions regarding potential use of RNAi as therapeutic applications. Our massive parallelized pair alignment scoring between dsRNA in Genebank and expressed sequence tags (ESTs) in Caenorhabditis elegans Genome Sequencing Projects revealed that this provides a useful tool for the prediction of RNAi induced cosuppression details for practical use. This pair alignment scoring method using high performance computing exhibited some possibility that numerous unwanted gene silencing and cosuppression exist even at high matching scores each other. The classifying the relative higher matching score of them based on GO (Gene Ontology) system could present mapping dsRNA of C. elegans and functional roles in an applied system. Our prediction also exhibited that more than 78% of the predicted co-suppressible genes are located in the ribosomal spot of C. elegans.
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KEYWORD
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RNA interference (RNAi), Expressed Sequence Tag (EST), in silico Biology, Multiple Sequence Alignment, Cosuppression, dsRNA, Caenorhabditis elegans
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