siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction
RNA interference (RNAi) is a technique used for transgene-mediated gene silencing based on the mechanism of posttranscriptional gene silencing (PTGS). PTGS is an ubiquitous basic biological phenomenon involved in the regulation of transcript abundance and plants’ immune response to viruses. PTGS als...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-08-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2019.01023/full |
| _version_ | 1818546153103294464 |
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| author | Stefanie Lück Tino Kreszies Marc Strickert Patrick Schweizer Markus Kuhlmann Dimitar Douchkov |
| author_facet | Stefanie Lück Tino Kreszies Marc Strickert Patrick Schweizer Markus Kuhlmann Dimitar Douchkov |
| author_sort | Stefanie Lück |
| collection | DOAJ |
| description | RNA interference (RNAi) is a technique used for transgene-mediated gene silencing based on the mechanism of posttranscriptional gene silencing (PTGS). PTGS is an ubiquitous basic biological phenomenon involved in the regulation of transcript abundance and plants’ immune response to viruses. PTGS also mediates genomic stability by silencing of retroelements. RNAi has become an important research tool for studying gene function by strong and selective suppression of target genes. Here, we present si-Fi, a software tool for design optimization of RNAi constructs necessary for specific target gene knock-down. It offers efficiency prediction of RNAi sequences and off-target search, required for the practical application of RNAi. si-Fi is an open-source (CC BY-SA license) desktop software that works in Microsoft Windows environment and can use custom sequence databases in standard FASTA format. |
| first_indexed | 2024-12-12T07:49:23Z |
| format | Article |
| id | doaj.art-2c3bfb6ec69744208af3596b005734cd |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-12T07:49:23Z |
| publishDate | 2019-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-2c3bfb6ec69744208af3596b005734cd2022-12-22T00:32:29ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2019-08-011010.3389/fpls.2019.01023450758siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target PredictionStefanie Lück0Tino Kreszies1Marc Strickert2Patrick Schweizer3Markus Kuhlmann4Dimitar Douchkov5Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, GermanyInstitute of Cellular and Molecular Botany, University of Bonn, Bonn, GermanyPhysics II Institute, University of Giessen, Giessen, GermanyLeibniz Institute of Plant Genetics and Crop Plant Research, Seeland, GermanyLeibniz Institute of Plant Genetics and Crop Plant Research, Seeland, GermanyLeibniz Institute of Plant Genetics and Crop Plant Research, Seeland, GermanyRNA interference (RNAi) is a technique used for transgene-mediated gene silencing based on the mechanism of posttranscriptional gene silencing (PTGS). PTGS is an ubiquitous basic biological phenomenon involved in the regulation of transcript abundance and plants’ immune response to viruses. PTGS also mediates genomic stability by silencing of retroelements. RNAi has become an important research tool for studying gene function by strong and selective suppression of target genes. Here, we present si-Fi, a software tool for design optimization of RNAi constructs necessary for specific target gene knock-down. It offers efficiency prediction of RNAi sequences and off-target search, required for the practical application of RNAi. si-Fi is an open-source (CC BY-SA license) desktop software that works in Microsoft Windows environment and can use custom sequence databases in standard FASTA format.https://www.frontiersin.org/article/10.3389/fpls.2019.01023/fullsi-FiRNA interfaceoff-targetRNAi designRNAi efficiency predictionposttranscriptional gene silencing |
| spellingShingle | Stefanie Lück Tino Kreszies Marc Strickert Patrick Schweizer Markus Kuhlmann Dimitar Douchkov siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction Frontiers in Plant Science si-Fi RNA interface off-target RNAi design RNAi efficiency prediction posttranscriptional gene silencing |
| title | siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction |
| title_full | siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction |
| title_fullStr | siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction |
| title_full_unstemmed | siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction |
| title_short | siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction |
| title_sort | sirna finder si fi software for rnai target design and off target prediction |
| topic | si-Fi RNA interface off-target RNAi design RNAi efficiency prediction posttranscriptional gene silencing |
| url | https://www.frontiersin.org/article/10.3389/fpls.2019.01023/full |
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