DC Field | Value | Language |
---|---|---|
dc.contributor.author | Kim, Hyerin | ko |
dc.contributor.author | Kang, NaNa | ko |
dc.contributor.author | An, KyuHyeon | ko |
dc.contributor.author | Koo, JaeHyung | ko |
dc.contributor.author | Kim, Min-Soo | ko |
dc.date.accessioned | 2020-03-19T03:21:21Z | - |
dc.date.available | 2020-03-19T03:21:21Z | - |
dc.date.created | 2020-03-10 | - |
dc.date.created | 2020-03-10 | - |
dc.date.issued | 2016-07 | - |
dc.identifier.citation | NUCLEIC ACIDS RESEARCH, v.44, no.W1, pp.W259 - W266 | - |
dc.identifier.issn | 0305-1048 | - |
dc.identifier.uri | http://hdl.handle.net/10203/272813 | - |
dc.description.abstract | Design of high-quality primers for multiple target sequences is essential for qPCR experiments, but is challenging due to the need to consider both homology tests on off-target sequences and the same stringent filtering constraints on the primers. Existing web servers for primer design have major drawbacks, including requiring the use of BLAST-like tools for homology tests, lack of support for ranking of primers, TaqMan probes and simultaneous design of primers against multiple targets. Due to the large-scale computational overhead, the few web servers supporting homology tests use heuristic approaches or perform homology tests within a limited scope. Here, we describe the MRPrimerW, which performs complete homology testing, supports batch design of primers for multi-target qPCR experiments, supports design of TaqMan probes and ranks the resulting primers to return the top-1 best primers to the user. To ensure high accuracy, we adopted the core algorithm of a previously reported MapReduce-based method, MRPrimer, but completely redesigned it to allow users to receive query results quickly in a web interface, without requiring a MapReduce cluster or a long computation. MRPrimerW provides primer design services and a complete set of 341 963 135 in silico validated primers covering 99% of human and mouse genes. Free access: http://MRPrimerW.com. | - |
dc.language | English | - |
dc.publisher | OXFORD UNIV PRESS | - |
dc.title | MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments | - |
dc.type | Article | - |
dc.identifier.wosid | 000379786800043 | - |
dc.identifier.scopusid | 2-s2.0-85021853308 | - |
dc.type.rims | ART | - |
dc.citation.volume | 44 | - |
dc.citation.issue | W1 | - |
dc.citation.beginningpage | W259 | - |
dc.citation.endingpage | W266 | - |
dc.citation.publicationname | NUCLEIC ACIDS RESEARCH | - |
dc.identifier.doi | 10.1093/nar/gkw380 | - |
dc.contributor.localauthor | Kim, Min-Soo | - |
dc.contributor.nonIdAuthor | Kim, Hyerin | - |
dc.contributor.nonIdAuthor | Kang, NaNa | - |
dc.contributor.nonIdAuthor | An, KyuHyeon | - |
dc.contributor.nonIdAuthor | Koo, JaeHyung | - |
dc.description.isOpenAccess | N | - |
dc.type.journalArticle | Article | - |
dc.subject.keywordPlus | REAL-TIME PCR | - |
dc.subject.keywordPlus | QUANTITATIVE GENE-EXPRESSION | - |
dc.subject.keywordPlus | POLYMERASE-CHAIN-REACTION | - |
dc.subject.keywordPlus | PROBE DATABASE | - |
dc.subject.keywordPlus | RTPRIMERDB | - |
dc.subject.keywordPlus | SEQUENCE | - |
dc.subject.keywordPlus | UPDATE | - |
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