sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database
<p>Abstract</p> <p>Background</p> <p>RNA interference has revolutionized our ability to study the effects of altering the expression of single genes in mammalian (and other) cells through targeted knockdown of gene expression. In this report we describe a web-based comp...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2007-05-01
|
| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/8/178 |
| _version_ | 1818582197347549184 |
|---|---|
| author | Garner Harold R Shah Jyoti K White Michael A Shames David S Minna John D |
| author_facet | Garner Harold R Shah Jyoti K White Michael A Shames David S Minna John D |
| author_sort | Garner Harold R |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>RNA interference has revolutionized our ability to study the effects of altering the expression of single genes in mammalian (and other) cells through targeted knockdown of gene expression. In this report we describe a web-based computational tool, siRNA Information Resource (sIR), which consists of a new open source database that contains validation information about published siRNA sequences and also provides a user-friendly interface to design and analyze siRNA sequences against a chosen target sequence.</p> <p>Results</p> <p>The siRNA design tool described in this paper employs empirically determined rules derived from a meta-analysis of the published data; it uses a weighted scoring system that determines the optimal sequence within a target mRNA and thus aids in the rational selection of siRNA sequences. This scoring system shows a non-linear correlation with the knockdown efficiency of siRNAs. sIR provides a fast, customized BLAST output for all selected siRNA sequences against a variety of databases so that the user can verify the uniqueness of the design. We have pre-designed siRNAs for all the known human genes (24,502) in the Refseq database. These siRNAs were pre-BLASTed against the human Unigene database to estimate the target specificity and all results are available online.</p> <p>Conclusion</p> <p>Although most of the rules for this scoring system were influenced by previously published rules, the weighted scoring system provides better flexibility in designing an appropriate siRNA when compared to the un-weighted scoring system. sIR is not only a comprehensive tool used to design siRNA sequences and lookup pre-designed siRNAs, but it is also a platform where researchers can share information on siRNA design and use.</p> |
| first_indexed | 2024-12-16T07:45:33Z |
| format | Article |
| id | doaj.art-b52aae7043534542b314afbcb61a6a80 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-16T07:45:33Z |
| publishDate | 2007-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-b52aae7043534542b314afbcb61a6a802022-12-21T22:38:58ZengBMCBMC Bioinformatics1471-21052007-05-018117810.1186/1471-2105-8-178sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA databaseGarner Harold RShah Jyoti KWhite Michael AShames David SMinna John D<p>Abstract</p> <p>Background</p> <p>RNA interference has revolutionized our ability to study the effects of altering the expression of single genes in mammalian (and other) cells through targeted knockdown of gene expression. In this report we describe a web-based computational tool, siRNA Information Resource (sIR), which consists of a new open source database that contains validation information about published siRNA sequences and also provides a user-friendly interface to design and analyze siRNA sequences against a chosen target sequence.</p> <p>Results</p> <p>The siRNA design tool described in this paper employs empirically determined rules derived from a meta-analysis of the published data; it uses a weighted scoring system that determines the optimal sequence within a target mRNA and thus aids in the rational selection of siRNA sequences. This scoring system shows a non-linear correlation with the knockdown efficiency of siRNAs. sIR provides a fast, customized BLAST output for all selected siRNA sequences against a variety of databases so that the user can verify the uniqueness of the design. We have pre-designed siRNAs for all the known human genes (24,502) in the Refseq database. These siRNAs were pre-BLASTed against the human Unigene database to estimate the target specificity and all results are available online.</p> <p>Conclusion</p> <p>Although most of the rules for this scoring system were influenced by previously published rules, the weighted scoring system provides better flexibility in designing an appropriate siRNA when compared to the un-weighted scoring system. sIR is not only a comprehensive tool used to design siRNA sequences and lookup pre-designed siRNAs, but it is also a platform where researchers can share information on siRNA design and use.</p>http://www.biomedcentral.com/1471-2105/8/178 |
| spellingShingle | Garner Harold R Shah Jyoti K White Michael A Shames David S Minna John D sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database BMC Bioinformatics |
| title | sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database |
| title_full | sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database |
| title_fullStr | sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database |
| title_full_unstemmed | sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database |
| title_short | sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database |
| title_sort | sir sirna information resource a web based tool for sirna sequence design and analysis and an open access sirna database |
| url | http://www.biomedcentral.com/1471-2105/8/178 |
| work_keys_str_mv | AT garnerharoldr sirsirnainformationresourceawebbasedtoolforsirnasequencedesignandanalysisandanopenaccesssirnadatabase AT shahjyotik sirsirnainformationresourceawebbasedtoolforsirnasequencedesignandanalysisandanopenaccesssirnadatabase AT whitemichaela sirsirnainformationresourceawebbasedtoolforsirnasequencedesignandanalysisandanopenaccesssirnadatabase AT shamesdavids sirsirnainformationresourceawebbasedtoolforsirnasequencedesignandanalysisandanopenaccesssirnadatabase AT minnajohnd sirsirnainformationresourceawebbasedtoolforsirnasequencedesignandanalysisandanopenaccesssirnadatabase |