PFRED: A computational platform for siRNA and antisense oligonucleotides design
PFRED a software application for the design, analysis, and visualization of antisense oligonucleotides and siRNA is described. The software provides an intuitive user-interface for scientists to design a library of siRNA or antisense oligonucleotides that target a specific gene of interest. Moreover...
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| Veröffentlicht in: | PloS one 2021-01, Vol.16 (1), p.e0238753-e0238753 |
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| creator | Sciabola, Simone Xi, Hualin Cruz, Dario Cao, Qing Lawrence, Christine Zhang, Tianhong Rotstein, Sergio Hughes, Jason D Caffrey, Daniel R Stanton, Robert V |
| description | PFRED a software application for the design, analysis, and visualization of antisense oligonucleotides and siRNA is described. The software provides an intuitive user-interface for scientists to design a library of siRNA or antisense oligonucleotides that target a specific gene of interest. Moreover, the tool facilitates the incorporation of various design criteria that have been shown to be important for stability and potency. PFRED has been made available as an open-source project so the code can be easily modified to address the future needs of the oligonucleotide research community. A compiled version is available for downloading at https://github.com/pfred/pfred-gui/releases/tag/v1.0 as a java Jar file. The source code and the links for downloading the precompiled version can be found at https://github.com/pfred. |
| doi_str_mv | 10.1371/journal.pone.0238753 |
| format | Article |
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The software provides an intuitive user-interface for scientists to design a library of siRNA or antisense oligonucleotides that target a specific gene of interest. Moreover, the tool facilitates the incorporation of various design criteria that have been shown to be important for stability and potency. PFRED has been made available as an open-source project so the code can be easily modified to address the future needs of the oligonucleotide research community. A compiled version is available for downloading at https://github.com/pfred/pfred-gui/releases/tag/v1.0 as a java Jar file. The source code and the links for downloading the precompiled version can be found at https://github.com/pfred.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0238753</identifier><identifier>PMID: 33481821</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Algorithms ; Alternative splicing ; Antisense oligonucleotides ; Antisense RNA ; Biology and life sciences ; Chemical modification ; Chemistry ; Complementarity ; Computational biology ; Computational Biology - methods ; Computer applications ; Data warehouses ; Design ; DNA Primers - genetics ; Enumeration ; FDA approval ; Gene Library ; Genetic research ; Genomics ; Graphical user interface ; Id protein ; Java ; Modules ; Nucleotides ; Oligonucleotides ; Oligonucleotides - genetics ; Oligonucleotides, Antisense - genetics ; Pharmaceutical sciences ; Properties ; Protein structure ; Research and Analysis Methods ; Ribonuclease H ; RNA, Small Interfering - genetics ; RNA-mediated interference ; Secondary structure ; Single-nucleotide polymorphism ; siRNA ; Software ; User interface ; User-Computer Interface</subject><ispartof>PloS one, 2021-01, Vol.16 (1), p.e0238753-e0238753</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 Sciabola et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2021 Sciabola et al 2021 Sciabola et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-70ba328c8068e1987485abb2a47d81ac048aade5b023325499c1b6d43b54c70e3</citedby><cites>FETCH-LOGICAL-c692t-70ba328c8068e1987485abb2a47d81ac048aade5b023325499c1b6d43b54c70e3</cites><orcidid>0000-0003-1448-3608</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7822268/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7822268/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2100,2926,23865,27923,27924,53790,53792,79371,79372</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33481821$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Kalendar, Ruslan</contributor><creatorcontrib>Sciabola, Simone</creatorcontrib><creatorcontrib>Xi, Hualin</creatorcontrib><creatorcontrib>Cruz, Dario</creatorcontrib><creatorcontrib>Cao, Qing</creatorcontrib><creatorcontrib>Lawrence, Christine</creatorcontrib><creatorcontrib>Zhang, Tianhong</creatorcontrib><creatorcontrib>Rotstein, Sergio</creatorcontrib><creatorcontrib>Hughes, Jason D</creatorcontrib><creatorcontrib>Caffrey, Daniel R</creatorcontrib><creatorcontrib>Stanton, Robert V</creatorcontrib><title>PFRED: A computational platform for siRNA and antisense oligonucleotides design</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>PFRED a software application for the design, analysis, and visualization of antisense oligonucleotides and siRNA is described. The software provides an intuitive user-interface for scientists to design a library of siRNA or antisense oligonucleotides that target a specific gene of interest. Moreover, the tool facilitates the incorporation of various design criteria that have been shown to be important for stability and potency. PFRED has been made available as an open-source project so the code can be easily modified to address the future needs of the oligonucleotide research community. A compiled version is available for downloading at https://github.com/pfred/pfred-gui/releases/tag/v1.0 as a java Jar file. 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| subjects | Algorithms Alternative splicing Antisense oligonucleotides Antisense RNA Biology and life sciences Chemical modification Chemistry Complementarity Computational biology Computational Biology - methods Computer applications Data warehouses Design DNA Primers - genetics Enumeration FDA approval Gene Library Genetic research Genomics Graphical user interface Id protein Java Modules Nucleotides Oligonucleotides Oligonucleotides - genetics Oligonucleotides, Antisense - genetics Pharmaceutical sciences Properties Protein structure Research and Analysis Methods Ribonuclease H RNA, Small Interfering - genetics RNA-mediated interference Secondary structure Single-nucleotide polymorphism siRNA Software User interface User-Computer Interface |
| title | PFRED: A computational platform for siRNA and antisense oligonucleotides design |
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