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mysirna-designer a workflow for efficient sirna designmysirna-designer有效的核设计的工作流.pdf

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mysirna-designer a workflow for efficient sirna designmysirna-designer有效的核设计的工作流

MysiRNA-Designer: A Workflow for Efficient siRNA Design 1,2,4 3 1,2,3 Mohamed Mysara *, Jonathan M. Garibaldi *, Mahmoud ElHefnawi * 1 Informatics and Systems Department and Biomedical Informatics and Chemoinformatics Group, Division of Engineering Research and Centre of Excellence for Advanced Sciences, National Research Centre, Cairo, Egypt, 2 Information Technology Institute, Division of Biomedical Informatics and Bioinformatics, Smart Village, 6th of October City, Egypt, 3 Computer Science and Engineering Department, Egypt-Japan University of Science and Technology (E-JUST), Alexandria, Egypt, 4 Intelligent Modeling and Analysis Research Group, School of Computer Science, University of Nottingham, Nottingham, United Kingdom Abstract 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-D