In-silico Approaches for RNAi Post-Transcriptional Gene Regulation: Optimizing siRNA Design and Selection

ElHefnawi, Mahmoud; Mysara, Mohamed

doi:10.5772/18455

Cited by 4 publications

(2 citation statements)

References 44 publications

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“…The comparison included stages implemented in each tool, such as the tool's ability to consider multiple transcripts and select conserved region analysis, Target accessibility evaluation, SNPs, and Off-target filtration covering both complete (full homology) and partial (seed region) filtration [ Table 3 ]. These steps represent state of the art approaches for efficient design of siRNAs [41] . As illustrated, MysiRNA-Designer performs all of the above mentioned steps required for efficient siRNA design, while the other tools do lack some of the mentioned criteria.…”

Section: Resultsmentioning

confidence: 99%

MysiRNA-Designer: A Workflow for Efficient siRNA Design

2011

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The design of small interfering RNA (siRNA) is a multi factorial problem that has gained the attention of many researchers in the area of therapeutic and functional genomics. MysiRNA score was previously introduced that improves the correlation of siRNA activity prediction considering state of the art algorithms. In this paper, a new program, MysiRNA-Designer, is described which integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches. It also features the MysiRNA score, a highly ranked correlated siRNA efficacy prediction score for ranking the designed siRNAs, in addition to top scoring models Biopredsi, DISR, Thermocomposition21 and i-Score, and integrates them in a unique siRNA score-filtration technique. This multi-score filtration layer filters siRNA that passes the 90% thresholds calculated from experimental dataset features. MysiRNA-Designer takes an accession, finds conserved regions among its transcript space, finds accessible regions within the mRNA, designs all possible siRNAs for these regions, filters them based on multi-scores thresholds, and then performs SNP and off-target filtration. These strict selection criteria were tested against human genes in which at least one active siRNA was designed from 95.7% of total genes. In addition, when tested against an experimental dataset, MysiRNA-Designer was found capable of rejecting 98% of the false positive siRNAs, showing superiority over three state of the art siRNA design programs. MysiRNA is a freely accessible (Microsoft Windows based) desktop application that can be used to design siRNA with a high accuracy and specificity. We believe that MysiRNA-Designer has the potential to play an important role in this area.

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Section: Resultsmentioning

confidence: 99%

MysiRNA-Designer: A Workflow for Efficient siRNA Design

2011

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“…Various programs are now available for siRNA full automation designing which include MysiRNA‐Designer, siDESIGN Center, Asi‐Designer, RNAxs, siDRM . Numerous factors are involved in siRNA designing process and due consideration must be given to them for achieving desired siRNA, which have been depicted in Figure with the sub‐factors associated with them.…”

Section: Mechanism Of Sirna and Its Designingmentioning

confidence: 99%

Therapeutic implications of small interfering RNA in cardiovascular diseases

Raghunathan

Patel

2012

Fundamemntal Clinical Pharma

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Cardiovascular diseases (CVDs) place a heavy burden on the economies of low- and middle-income countries. Comprehensive action requires combining approaches that seek to reduce the risks throughout the entire population with strategies that target individuals at high risk or with established disease. Small interfering RNA (siRNA) as a functional mediator for regulation of gene expression has been evaluated for potential therapeutic targets for the treatment of various cardiovascular diseases such as hypertension, atherosclerosis, heart failure etc. The present review attempts have been made to provide a brief outline of the current understanding of the mechanism of RNAi and the delivery system and describe the therapeutic application of siRNAs and their potential for treating CVDs which are taking a heavy toll on human life.

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Plant Bioinformatics: Next Generation Sequencing Approaches

Filippis

2017

Plant Bioinformatics

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In-silico Approaches for RNAi Post-Transcriptional Gene Regulation: Optimizing siRNA Design and Selection

Cited by 4 publications

References 44 publications

MysiRNA-Designer: A Workflow for Efficient siRNA Design

MysiRNA-Designer: A Workflow for Efficient siRNA Design

Therapeutic implications of small interfering RNA in cardiovascular diseases

Plant Bioinformatics: Next Generation Sequencing Approaches

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