{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T12:15:44Z","timestamp":1774786544191,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Artificially synthesized short interfering RNAs (siRNAs) are widely used in functional genomics to knock down specific target genes. One ongoing challenge is to guarantee that the siRNA does not elicit off-target effects. Initial reports suggested that siRNAs were highly sequence-specific; however, subsequent data indicates that this is not necessarily the case. It is still uncertain what level of similarity and other rules are required for an off-target effect to be observed, and scoring schemes have not been developed to look beyond simple measures such as the number of mismatches or the number of consecutive matching bases present.<\/jats:p>\n               <jats:p>We created design rules for predicting the likelihood of a non-specific effect and present a web server that allows the user to check the specificity of a given siRNA in a flexible manner using a combination of methods. The server finds potential off-target matches in the corresponding RefSeq database and ranks them according to a scoring system based on experimental studies of specificity.<\/jats:p>\n               <jats:p>Availability: The server is available at<\/jats:p>\n               <jats:p>http:\/\/informatics-eskitis.griffith.edu.au\/SpecificityServer.<\/jats:p>\n               <jats:p>Contact: \u00a0Erik.Sonnhammer@sbc.su.se<\/jats:p>\n               <jats:p>Supplementary information: Supplementary analysis and figures are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn121","type":"journal-article","created":{"date-parts":[[2008,4,9]],"date-time":"2008-04-09T00:14:59Z","timestamp":1207700099000},"page":"1316-1317","source":"Crossref","is-referenced-by-count":14,"title":["siRNA specificity searching incorporating mismatch tolerance data"],"prefix":"10.1093","volume":"24","author":[{"given":"Alistair M.","family":"Chalk","sequence":"first","affiliation":[{"name":"1 Department of Cell and Molecular Biology, Karolinska Institutet, S-171 77 Stockholm and 2Stockholm Bioinformatics Center, Stockholm University, S-106 91 Stockholm, Sweden"}]},{"given":"Erik L. L.","family":"Sonnhammer","sequence":"additional","affiliation":[{"name":"1 Department of Cell and Molecular Biology, Karolinska Institutet, S-171 77 Stockholm and 2Stockholm Bioinformatics Center, Stockholm University, S-106 91 Stockholm, Sweden"},{"name":"1 Department of Cell and Molecular Biology, Karolinska Institutet, S-171 77 Stockholm and 2Stockholm Bioinformatics Center, Stockholm University, S-106 91 Stockholm, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2008,4,7]]},"reference":[{"key":"2023020210033906600_B1","doi-asserted-by":"crossref","first-page":"6877","DOI":"10.1093\/emboj\/20.23.6877","article-title":"Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate","volume":"20","author":"Elbashir","year":"2001","journal-title":"EMBO J"},{"key":"2023020210033906600_B2","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1101\/gad.1184404","article-title":"Specificity of microRNA target selection in translational repression","volume":"18","author":"Doench","year":"2004","journal-title":"Genes Dev"},{"key":"2023020210033906600_B3","doi-asserted-by":"crossref","first-page":"1671","DOI":"10.1093\/nar\/gki312","article-title":"A systematic analysis of the silencing effects of an active siRNA at all single-nucleotide mismatched target sites","volume":"33","author":"Du","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2023020210033906600_B4","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1038\/nsmb780","article-title":"Kinetic analysis of the RNAi enzyme complex","volume":"11","author":"Haley","year":"2004","journal-title":"Nat. Struct. Mol. Biol"},{"key":"2023020210033906600_B5","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1038\/nbt831","article-title":"Expression profiling reveals off-target gene regulation by RNAi","volume":"21","author":"Jackson","year":"2003","journal-title":"Nat. Biotechnol"},{"key":"2023020210033906600_B6","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1101\/gad.1284105","article-title":"Perspective: machines for RNAi","volume":"19","author":"Tomari","year":"2005","journal-title":"Genes Dev"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/10\/1316\/49046617\/bioinformatics_24_10_1316.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/10\/1316\/49046617\/bioinformatics_24_10_1316.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T10:09:12Z","timestamp":1675332552000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/10\/1316\/178454"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,4,7]]},"references-count":6,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2008,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn121","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,5,15]]},"published":{"date-parts":[[2008,4,7]]}}}