ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites
<p>Abstract</p> <p>Background</p> <p>Zinc Finger Nucleases (ZFNs) are man-made restriction enzymes useful for manipulating genomes by cleaving target DNA sequences. ZFNs allow therapeutic gene correction or creation of genetically modified model organisms. ZFN specifici...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2011-05-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/12/152 |
| _version_ | 1818645429442576384 |
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| author | Iseli Christian Ambrosini Giovanna Cradick Thomas J Bucher Philipp McCaffrey Anton P |
| author_facet | Iseli Christian Ambrosini Giovanna Cradick Thomas J Bucher Philipp McCaffrey Anton P |
| author_sort | Iseli Christian |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Zinc Finger Nucleases (ZFNs) are man-made restriction enzymes useful for manipulating genomes by cleaving target DNA sequences. ZFNs allow therapeutic gene correction or creation of genetically modified model organisms. ZFN specificity is not absolute; therefore, it is essential to select ZFN target sites without similar genomic off-target sites. It is important to assay for off-target cleavage events at sites similar to the target sequence.</p> <p>Results</p> <p>ZFN-Site is a web interface that searches multiple genomes for ZFN off-target sites. Queries can be based on the target sequence or can be expanded using degenerate specificity to account for known ZFN binding preferences. ZFN off-target sites are outputted with links to genome browsers, facilitating off-target cleavage site screening. We verified ZFN-Site using previously published ZFN half-sites and located their target sites and their previously described off-target sites. While we have tailored this tool to ZFNs, ZFN-Site can also be used to find potential off-target sites for other nucleases, such as TALE nucleases.</p> <p>Conclusions</p> <p>ZFN-Site facilitates genome searches for possible ZFN cleavage sites based on user-defined stringency limits. ZFN-Site is an improvement over other methods because the FetchGWI search engine uses an indexed search of genome sequences for all ZFN target sites and possible off-target sites matching the half-sites and stringency limits. Therefore, ZFN-Site does not miss potential off-target sites.</p> |
| first_indexed | 2024-12-17T00:30:36Z |
| format | Article |
| id | doaj.art-a590cdf9ad934c239f63311c2328ee09 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-17T00:30:36Z |
| publishDate | 2011-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-a590cdf9ad934c239f63311c2328ee092022-12-21T22:10:19ZengBMCBMC Bioinformatics1471-21052011-05-0112115210.1186/1471-2105-12-152ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sitesIseli ChristianAmbrosini GiovannaCradick Thomas JBucher PhilippMcCaffrey Anton P<p>Abstract</p> <p>Background</p> <p>Zinc Finger Nucleases (ZFNs) are man-made restriction enzymes useful for manipulating genomes by cleaving target DNA sequences. ZFNs allow therapeutic gene correction or creation of genetically modified model organisms. ZFN specificity is not absolute; therefore, it is essential to select ZFN target sites without similar genomic off-target sites. It is important to assay for off-target cleavage events at sites similar to the target sequence.</p> <p>Results</p> <p>ZFN-Site is a web interface that searches multiple genomes for ZFN off-target sites. Queries can be based on the target sequence or can be expanded using degenerate specificity to account for known ZFN binding preferences. ZFN off-target sites are outputted with links to genome browsers, facilitating off-target cleavage site screening. We verified ZFN-Site using previously published ZFN half-sites and located their target sites and their previously described off-target sites. While we have tailored this tool to ZFNs, ZFN-Site can also be used to find potential off-target sites for other nucleases, such as TALE nucleases.</p> <p>Conclusions</p> <p>ZFN-Site facilitates genome searches for possible ZFN cleavage sites based on user-defined stringency limits. ZFN-Site is an improvement over other methods because the FetchGWI search engine uses an indexed search of genome sequences for all ZFN target sites and possible off-target sites matching the half-sites and stringency limits. Therefore, ZFN-Site does not miss potential off-target sites.</p>http://www.biomedcentral.com/1471-2105/12/152 |
| spellingShingle | Iseli Christian Ambrosini Giovanna Cradick Thomas J Bucher Philipp McCaffrey Anton P ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites BMC Bioinformatics |
| title | ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites |
| title_full | ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites |
| title_fullStr | ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites |
| title_full_unstemmed | ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites |
| title_short | ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites |
| title_sort | zfn site searches genomes for zinc finger nuclease target sites and off target sites |
| url | http://www.biomedcentral.com/1471-2105/12/152 |
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