siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction
نویسندگان
چکیده
منابع مشابه
Accelerated off-target search algorithm for siRNA
MOTIVATION Designing highly effective short interfering RNA (siRNA) sequences with maximum target-specificity for mammalian RNA interference (RNAi) is one of the hottest topics in molecular biology. The relationship between siRNA sequences and RNAi activity has been studied extensively to establish rules for selecting highly effective sequences. However, there is a pressing need to compute siRN...
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RNA interference (RNAi) is a mechanism through which small interfering RNA (siRNA) induces sequence-specific posttranscriptional gene silencing. RNAi is commonly recognized as a powerful tool not only for functional genomics but also for therapeutic applications. Twenty-one-nucleotide-long siRNA suppresses the expression of the intended gene whose transcript possesses perfect complementarity to...
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The downregulation of many mRNAs has been observed through bioinformatic analysis of microarray results following transfection of short interfering RNAs (siRNAs). Many of these mRNA changes are due to the interaction of the siRNA guide strand with partially complementary sites and thus are considered "off-target" effects. To examine the mRNA:siRNA interactions important for off-target effects, ...
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Smith-Waterman alignment algorithm is favored in search for siRNA off-target instead of the BLAST algorithm, because BLAST tends to overlook some significant homologous sequences, especially when they are short (21 nt~27 nt). Smith-Waterman algorithm, however, suffers from its own shortcomings, especially its inefficiency in searching through a large sequence database. This paper presents a two...
متن کاملThe siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects
RNA interference (RNAi) is a powerful tool for post-transcriptional gene silencing. However, the siRNA guide strand may bind unintended off-target transcripts via partial sequence complementarity by a mechanism closely mirroring micro RNA (miRNA) silencing. To better understand these off-target effects, we investigated the correlation between sequence features within various subsections of siRN...
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ژورنال
عنوان ژورنال: Frontiers in Plant Science
سال: 2019
ISSN: 1664-462X
DOI: 10.3389/fpls.2019.01023