VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses.
Identifieur interne : 001084 ( PubMed/Curation ); précédent : 001083; suivant : 001085VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses.
Auteurs : Abid Qureshi ; Nishant Thakur ; Manoj Kumar [Inde]Source :
- Journal of translational medicine [ 1479-5876 ] ; 2013.
Descripteurs français
- KwdFr :
- Algorithmes, Bases de données génétiques, Conformation d'acide nucléique, Humains, Internet, Orthomyxoviridae (génétique), Orthomyxoviridae (isolement et purification), Petit ARN interférent (), Petit ARN interférent (génétique), Thermodynamique, VIH (Virus de l'Immunodéficience Humaine) (génétique), VIH (Virus de l'Immunodéficience Humaine) (isolement et purification), Virus de l'hépatite (génétique), Virus de l'hépatite (isolement et purification), Virus du SRAS (génétique), Virus du SRAS (isolement et purification).
- MESH :
- génétique : Orthomyxoviridae, Petit ARN interférent, VIH (Virus de l'Immunodéficience Humaine), Virus de l'hépatite, Virus du SRAS.
- isolement et purification : Orthomyxoviridae, VIH (Virus de l'Immunodéficience Humaine), Virus de l'hépatite, Virus du SRAS.
- Algorithmes, Bases de données génétiques, Conformation d'acide nucléique, Humains, Internet, Petit ARN interférent, Thermodynamique.
English descriptors
- KwdEn :
- Algorithms, Databases, Genetic, HIV (genetics), HIV (isolation & purification), Hepatitis Viruses (genetics), Hepatitis Viruses (isolation & purification), Humans, Internet, Nucleic Acid Conformation, Orthomyxoviridae (genetics), Orthomyxoviridae (isolation & purification), RNA, Small Interfering (chemistry), RNA, Small Interfering (genetics), SARS Virus (genetics), SARS Virus (isolation & purification), Thermodynamics.
- MESH :
- chemical , chemistry : RNA, Small Interfering.
- genetics : HIV, Hepatitis Viruses, Orthomyxoviridae, RNA, Small Interfering, SARS Virus.
- isolation & purification : HIV, Hepatitis Viruses, Orthomyxoviridae, SARS Virus.
- Algorithms, Databases, Genetic, Humans, Internet, Nucleic Acid Conformation, Thermodynamics.
Abstract
Selection of effective viral siRNA is an indispensable step in the development of siRNA based antiviral therapeutics. Despite immense potential, a viral siRNA efficacy prediction algorithm is still not available. Moreover, performances of the existing general mammalian siRNA efficacy predictors are not satisfactory for viral siRNAs. Therefore, we have developed "VIRsiRNApred" a support vector machine (SVM) based method for predicting the efficacy of viral siRNA.
DOI: 10.1186/1479-5876-11-305
PubMed: 24330765
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Thakur</name></author><author><name sortKey="Kumar, Manoj" sort="Kumar, Manoj" uniqKey="Kumar M" first="Manoj" last="Kumar">Manoj Kumar</name><affiliation wicri:level="1"><nlm:affiliation>Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39-A, Chandigarh 160036, India. manojk@imtech.res.in.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39-A, Chandigarh 160036</wicri:regionArea></affiliation></author></analytic><series><title level="j">Journal of translational medicine</title><idno type="eISSN">1479-5876</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Databases, Genetic</term><term>HIV (genetics)</term><term>HIV (isolation & purification)</term><term>Hepatitis Viruses (genetics)</term><term>Hepatitis Viruses (isolation & purification)</term><term>Humans</term><term>Internet</term><term>Nucleic Acid Conformation</term><term>Orthomyxoviridae (genetics)</term><term>Orthomyxoviridae (isolation & purification)</term><term>RNA, Small Interfering (chemistry)</term><term>RNA, Small Interfering (genetics)</term><term>SARS Virus (genetics)</term><term>SARS Virus (isolation & purification)</term><term>Thermodynamics</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Bases de données génétiques</term><term>Conformation d'acide nucléique</term><term>Humains</term><term>Internet</term><term>Orthomyxoviridae (génétique)</term><term>Orthomyxoviridae (isolement et purification)</term><term>Petit ARN interférent ()</term><term>Petit ARN interférent (génétique)</term><term>Thermodynamique</term><term>VIH (Virus de l'Immunodéficience Humaine) (génétique)</term><term>VIH (Virus de l'Immunodéficience Humaine) (isolement et purification)</term><term>Virus de l'hépatite (génétique)</term><term>Virus de l'hépatite (isolement et purification)</term><term>Virus du SRAS (génétique)</term><term>Virus du SRAS (isolement et purification)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA, Small Interfering</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>HIV</term><term>Hepatitis Viruses</term><term>Orthomyxoviridae</term><term>RNA, Small Interfering</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Orthomyxoviridae</term><term>Petit ARN interférent</term><term>VIH (Virus de l'Immunodéficience Humaine)</term><term>Virus de l'hépatite</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>HIV</term><term>Hepatitis Viruses</term><term>Orthomyxoviridae</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Orthomyxoviridae</term><term>VIH (Virus de l'Immunodéficience Humaine)</term><term>Virus de l'hépatite</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Databases, Genetic</term><term>Humans</term><term>Internet</term><term>Nucleic Acid Conformation</term><term>Thermodynamics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Bases de données génétiques</term><term>Conformation d'acide nucléique</term><term>Humains</term><term>Internet</term><term>Petit ARN interférent</term><term>Thermodynamique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Selection of effective viral siRNA is an indispensable step in the development of siRNA based antiviral therapeutics. Despite immense potential, a viral siRNA efficacy prediction algorithm is still not available. Moreover, performances of the existing general mammalian siRNA efficacy predictors are not satisfactory for viral siRNAs. Therefore, we have developed "VIRsiRNApred" a support vector machine (SVM) based method for predicting the efficacy of viral siRNA.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24330765</PMID><DateCompleted><Year>2014</Year><Month>09</Month><Day>26</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1479-5876</ISSN><JournalIssue CitedMedium="Internet"><Volume>11</Volume><PubDate><Year>2013</Year><Month>Dec</Month><Day>11</Day></PubDate></JournalIssue><Title>Journal of translational medicine</Title><ISOAbbreviation>J Transl Med</ISOAbbreviation></Journal><ArticleTitle>VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses.</ArticleTitle><Pagination><MedlinePgn>305</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1479-5876-11-305</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Selection of effective viral siRNA is an indispensable step in the development of siRNA based antiviral therapeutics. Despite immense potential, a viral siRNA efficacy prediction algorithm is still not available. Moreover, performances of the existing general mammalian siRNA efficacy predictors are not satisfactory for viral siRNAs. Therefore, we have developed "VIRsiRNApred" a support vector machine (SVM) based method for predicting the efficacy of viral siRNA.</AbstractText><AbstractText Label="METHODS" NlmCategory="METHODS">In the present study, we have employed a new dataset of 1725 viral siRNAs with experimentally verified quantitative efficacies tested under heterogeneous experimental conditions and targeting as many as 37 important human viruses including HIV, Influenza, HCV, HBV, SARS etc. These siRNAs were divided into training (T1380) and validation (V345) datasets. Important siRNA sequence features including mono to penta nucleotide frequencies, binary pattern, thermodynamic properties and secondary structure were employed for model development.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">During 10-fold cross validation on T1380 using hybrid approach, we achieved a maximum Pearson Correlation Coefficient (PCC) of 0.55 between predicted and actual efficacy of viral siRNAs. On V345 independent dataset, our best model achieved a maximum correlation of 0.50 while existing general siRNA prediction methods showed PCC from 0.05 to 0.18. However, using leave one out cross validation PCC was improved to 0.58 and 0.55 on training and validation datasets respectively. SVM performed better than other machine learning techniques used like ANN, KNN and REP Tree.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">VIRsiRNApred is the first algorithm for predicting inhibition efficacy of viral siRNAs which is developed using experimentally verified viral siRNAs. We hope this algorithm would be useful in predicting highly potent viral siRNA to aid siRNA based antiviral therapeutics development. The web server is freely available at http://crdd.osdd.net/servers/virsirnapred/.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Qureshi</LastName><ForeName>Abid</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Thakur</LastName><ForeName>Nishant</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Kumar</LastName><ForeName>Manoj</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39-A, Chandigarh 160036, India. manojk@imtech.res.in.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D023361">Validation Study</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>12</Month><Day>11</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>J Transl Med</MedlineTA><NlmUniqueID>101190741</NlmUniqueID><ISSNLinking>1479-5876</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D034741">RNA, Small Interfering</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="N">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D030541" MajorTopicYN="Y">Databases, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006678" MajorTopicYN="N">HIV</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006518" MajorTopicYN="N">Hepatitis 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