String Kernels of Imperfect Matches for Off-target Detection in RNA Interference
RNA interference (RNAi) is a posttranscriptional gene silencing mechanism frequently used to study gene functions and knock down viral genes. RNAi has been regarded as a highly effective means of gene repression. However, an “off-target effect” deteriorates its specificity and applicability. The com...
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| creator | Qiu, Shibin Lane, Terran |
| description | RNA interference (RNAi) is a posttranscriptional gene silencing mechanism frequently used to study gene functions and knock down viral genes. RNAi has been regarded as a highly effective means of gene repression. However, an “off-target effect” deteriorates its specificity and applicability. The complete off-target effects can only be characterized by examining all factors through systematic investigation of each gene in a genome. However, this complete investigation is too expensive to conduct experimentally which motivates a computational study. The sequence matching between an siRNA and its target mRNA allows for mismatches, G-U wobbles, and the secondary structure bulges, in addition to exact matches. To simulate these matching features, we propose string kernels measuring the similarity between two oligonucleotides and develop novel efficient implementations for RNAi off-target detection. We apply the algorithms for off-target errors in C. elegans and human. |
| doi_str_mv | 10.1007/11428848_114 |
| format | Conference Proceeding |
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To simulate these matching features, we propose string kernels measuring the similarity between two oligonucleotides and develop novel efficient implementations for RNAi off-target detection. We apply the algorithms for off-target errors in C. elegans and human.</description><identifier>ISSN: 0302-9743</identifier><identifier>ISBN: 9783540260431</identifier><identifier>ISBN: 3540260439</identifier><identifier>ISBN: 3540260323</identifier><identifier>ISBN: 9783540260325</identifier><identifier>EISSN: 1611-3349</identifier><identifier>EISBN: 9783540321149</identifier><identifier>EISBN: 3540321144</identifier><identifier>DOI: 10.1007/11428848_114</identifier><language>eng</language><publisher>Berlin, Heidelberg: Springer Berlin Heidelberg</publisher><subject>Algorithmics. Computability. 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A.</contributor><creatorcontrib>Qiu, Shibin</creatorcontrib><creatorcontrib>Lane, Terran</creatorcontrib><title>String Kernels of Imperfect Matches for Off-target Detection in RNA Interference</title><title>Computational Science – ICCS 2005</title><description>RNA interference (RNAi) is a posttranscriptional gene silencing mechanism frequently used to study gene functions and knock down viral genes. RNAi has been regarded as a highly effective means of gene repression. However, an “off-target effect” deteriorates its specificity and applicability. The complete off-target effects can only be characterized by examining all factors through systematic investigation of each gene in a genome. However, this complete investigation is too expensive to conduct experimentally which motivates a computational study. The sequence matching between an siRNA and its target mRNA allows for mismatches, G-U wobbles, and the secondary structure bulges, in addition to exact matches. To simulate these matching features, we propose string kernels measuring the similarity between two oligonucleotides and develop novel efficient implementations for RNAi off-target detection. We apply the algorithms for off-target errors in C. elegans and human.</description><subject>Algorithmics. Computability. Computer arithmetics</subject><subject>Applied sciences</subject><subject>Binary Search Tree</subject><subject>Computer science; control theory; systems</subject><subject>Exact Match</subject><subject>Exact sciences and technology</subject><subject>RNAi Experiment</subject><subject>String Kernel</subject><subject>Study Gene Function</subject><subject>Theoretical computing</subject><issn>0302-9743</issn><issn>1611-3349</issn><isbn>9783540260431</isbn><isbn>3540260439</isbn><isbn>3540260323</isbn><isbn>9783540260325</isbn><isbn>9783540321149</isbn><isbn>3540321144</isbn><fulltext>true</fulltext><rsrctype>conference_proceeding</rsrctype><creationdate>2005</creationdate><recordtype>conference_proceeding</recordtype><recordid>eNpNkElPwzAQhc0mUUpv_ABfuCAFxkuc-FiVraJQxHK2XHdcAq0T2b7w70lVhDjN8r550jxCzhhcMoDqijHJ61rWpm_2yEhXtSglCN6Pep8MmGKsEELqgz-NK5CCHZIBCOCFrqQ4JicpfQIArzQfkOfXHJuwog8YA64TbT2dbjqMHl2mjza7D0zUt5HOvS-yjSvM9BpzrzZtoE2gL09jOg15exExODwlR96uE45-65C83968Te6L2fxuOhnPCseVyIVztgZAB6xE75QspfRLDgy8d8IiWCWcqPrVUi-tArvgyvWEKBcIrK5BDMn5zrezydm1jza4JpkuNhsbvw1TWrNSy5672HGp2z6K0Sza9isZBmabqfmfqfgB5wpjcQ</recordid><startdate>2005</startdate><enddate>2005</enddate><creator>Qiu, Shibin</creator><creator>Lane, Terran</creator><general>Springer Berlin Heidelberg</general><general>Springer</general><scope>IQODW</scope></search><sort><creationdate>2005</creationdate><title>String Kernels of Imperfect Matches for Off-target Detection in RNA Interference</title><author>Qiu, Shibin ; Lane, Terran</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c263t-cca800ec015efc64544fd2010ffc3ae0a63c37fd2d9da60ab26c4fd35be018803</frbrgroupid><rsrctype>conference_proceedings</rsrctype><prefilter>conference_proceedings</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Algorithmics. Computability. Computer arithmetics</topic><topic>Applied sciences</topic><topic>Binary Search Tree</topic><topic>Computer science; control theory; systems</topic><topic>Exact Match</topic><topic>Exact sciences and technology</topic><topic>RNAi Experiment</topic><topic>String Kernel</topic><topic>Study Gene Function</topic><topic>Theoretical computing</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Qiu, Shibin</creatorcontrib><creatorcontrib>Lane, Terran</creatorcontrib><collection>Pascal-Francis</collection></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Qiu, Shibin</au><au>Lane, Terran</au><au>Dongarra, Jack J.</au><au>van Albada, Geert Dick</au><au>Sunderam, Vaidy S.</au><au>Sloot, Peter M. A.</au><format>book</format><genre>proceeding</genre><ristype>CONF</ristype><atitle>String Kernels of Imperfect Matches for Off-target Detection in RNA Interference</atitle><btitle>Computational Science – ICCS 2005</btitle><date>2005</date><risdate>2005</risdate><spage>894</spage><epage>902</epage><pages>894-902</pages><issn>0302-9743</issn><eissn>1611-3349</eissn><isbn>9783540260431</isbn><isbn>3540260439</isbn><isbn>3540260323</isbn><isbn>9783540260325</isbn><eisbn>9783540321149</eisbn><eisbn>3540321144</eisbn><abstract>RNA interference (RNAi) is a posttranscriptional gene silencing mechanism frequently used to study gene functions and knock down viral genes. RNAi has been regarded as a highly effective means of gene repression. However, an “off-target effect” deteriorates its specificity and applicability. The complete off-target effects can only be characterized by examining all factors through systematic investigation of each gene in a genome. However, this complete investigation is too expensive to conduct experimentally which motivates a computational study. The sequence matching between an siRNA and its target mRNA allows for mismatches, G-U wobbles, and the secondary structure bulges, in addition to exact matches. To simulate these matching features, we propose string kernels measuring the similarity between two oligonucleotides and develop novel efficient implementations for RNAi off-target detection. We apply the algorithms for off-target errors in C. elegans and human.</abstract><cop>Berlin, Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><doi>10.1007/11428848_114</doi><tpages>9</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0302-9743 |
| ispartof | Computational Science – ICCS 2005, 2005, p.894-902 |
| issn | 0302-9743 1611-3349 |
| language | eng |
| recordid | cdi_pascalfrancis_primary_16991594 |
| source | Springer Books |
| subjects | Algorithmics. Computability. Computer arithmetics Applied sciences Binary Search Tree Computer science control theory systems Exact Match Exact sciences and technology RNAi Experiment String Kernel Study Gene Function Theoretical computing |
| title | String Kernels of Imperfect Matches for Off-target Detection in RNA Interference |
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