Accelerated off-target search algorithm for siRNA
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...
متن کاملFast and Complete Search of siRNA Off-target Sequences
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 کاملA Database-Based Two-Phase Algorithm For Efficient and Complete Detection of siRNA Off-Target Homology
Since the discovery of RNA Interference (RNAi), a cellular phenomenon in which a small double stranded RNA induces the degradation of its sequence specific target mRNA, using a computer-aided software tool to help design functional small interfering RNA (siRNA) or small hairpin RNA (shRNA) has become a standard procedure in applying RNAi to silence a target gene. A critical consideration in siR...
متن کاملComparison of siRNA-induced off-target RNA and protein effects.
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, ...
متن کاملWhole-Genome Thermodynamic Analysis Reduces siRNA Off-Target Effects
Small interfering RNAs (siRNAs) are important tools for knocking down targeted genes, and have been widely applied to biological and biomedical research. To design siRNAs, two important aspects must be considered: the potency in knocking down target genes and the off-target effect on any nontarget genes. Although many studies have produced useful tools to design potent siRNAs, off-target preven...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2004
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/bti155