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Cas-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9.

Park J, Kim JS, Bae S - Bioinformatics (2016)

Bottom Line: We develop an online tool, Cas-Database, a genome-wide gRNA library design tool for Cas9 nucleases from Streptococcus pyogenes (SpCas9).With an easy-to-use web interface, Cas-Database allows users to select optimal target sequences simply by changing the filtering conditions.Cas-Database also provides a web application programming interface (web API) for advanced bioinformatics users.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Hanyang University, Seoul 133-791, South Korea.

No MeSH data available.


Related in: MedlinePlus

The ‘Quick Info’ function of Cas-Database. The ‘Add to Collection’ function of Cas-Database. (A) Cas-Database provides a unique and easy way to select many genes at once by the implementation of a ‘cart’ system. Users can collect desired genes by clicking on the ‘Add to Collection’ button or by uploading a text file as described in the Figure 1C legend. Note that one can also select genes from different organisms. By clicking on the ‘Select optimal gRNAs’ button, users will proceed to the next step. (B) The results page will list all available sgRNAs filtered by the default conditions on the top panel. A colored indicator represents the selection status for each gene, e.g. green (selected completely), yellow (selected partially) or red (not selected at all). A user can download only the genes for which sgRNAs were successfully designed, and repeat the process for the remaining genes by changing the filter criteria and clicking on the ‘Remove “green” genes from list’ button
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btw103-F3: The ‘Quick Info’ function of Cas-Database. The ‘Add to Collection’ function of Cas-Database. (A) Cas-Database provides a unique and easy way to select many genes at once by the implementation of a ‘cart’ system. Users can collect desired genes by clicking on the ‘Add to Collection’ button or by uploading a text file as described in the Figure 1C legend. Note that one can also select genes from different organisms. By clicking on the ‘Select optimal gRNAs’ button, users will proceed to the next step. (B) The results page will list all available sgRNAs filtered by the default conditions on the top panel. A colored indicator represents the selection status for each gene, e.g. green (selected completely), yellow (selected partially) or red (not selected at all). A user can download only the genes for which sgRNAs were successfully designed, and repeat the process for the remaining genes by changing the filter criteria and clicking on the ‘Remove “green” genes from list’ button

Mentions: Cas-Database also provides a novel function that allows the selection of sgRNAs from hundreds or thousands of genes at once through the use of a ‘cart’ system. Users can either collect desired genes on the main web page by clicking on the ‘Add to Collection’ button (Fig. 3A) or by uploading a text file as discussed above and shown in Figure 1C. After all desired genes are collected, clicking on the ‘Select optimal sgRNAs’ button will open the results page, which will list all available sgRNAs filtered by the default conditions as shown in Figure 3B. Users can easily change the filtering conditions, including the total count of sgRNAs for each gene, in the filter section that appears at the top of the resulting page (Fig. 3B). Because the AJAX technique is used, the retrieving processes run independently of each other, resulting in fast loading speeds; e.g. the loading time for 1000 genes is about 2 min in the default conditions.Fig. 3.


Cas-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9.

Park J, Kim JS, Bae S - Bioinformatics (2016)

The ‘Quick Info’ function of Cas-Database. The ‘Add to Collection’ function of Cas-Database. (A) Cas-Database provides a unique and easy way to select many genes at once by the implementation of a ‘cart’ system. Users can collect desired genes by clicking on the ‘Add to Collection’ button or by uploading a text file as described in the Figure 1C legend. Note that one can also select genes from different organisms. By clicking on the ‘Select optimal gRNAs’ button, users will proceed to the next step. (B) The results page will list all available sgRNAs filtered by the default conditions on the top panel. A colored indicator represents the selection status for each gene, e.g. green (selected completely), yellow (selected partially) or red (not selected at all). A user can download only the genes for which sgRNAs were successfully designed, and repeat the process for the remaining genes by changing the filter criteria and clicking on the ‘Remove “green” genes from list’ button
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4920116&req=5

btw103-F3: The ‘Quick Info’ function of Cas-Database. The ‘Add to Collection’ function of Cas-Database. (A) Cas-Database provides a unique and easy way to select many genes at once by the implementation of a ‘cart’ system. Users can collect desired genes by clicking on the ‘Add to Collection’ button or by uploading a text file as described in the Figure 1C legend. Note that one can also select genes from different organisms. By clicking on the ‘Select optimal gRNAs’ button, users will proceed to the next step. (B) The results page will list all available sgRNAs filtered by the default conditions on the top panel. A colored indicator represents the selection status for each gene, e.g. green (selected completely), yellow (selected partially) or red (not selected at all). A user can download only the genes for which sgRNAs were successfully designed, and repeat the process for the remaining genes by changing the filter criteria and clicking on the ‘Remove “green” genes from list’ button
Mentions: Cas-Database also provides a novel function that allows the selection of sgRNAs from hundreds or thousands of genes at once through the use of a ‘cart’ system. Users can either collect desired genes on the main web page by clicking on the ‘Add to Collection’ button (Fig. 3A) or by uploading a text file as discussed above and shown in Figure 1C. After all desired genes are collected, clicking on the ‘Select optimal sgRNAs’ button will open the results page, which will list all available sgRNAs filtered by the default conditions as shown in Figure 3B. Users can easily change the filtering conditions, including the total count of sgRNAs for each gene, in the filter section that appears at the top of the resulting page (Fig. 3B). Because the AJAX technique is used, the retrieving processes run independently of each other, resulting in fast loading speeds; e.g. the loading time for 1000 genes is about 2 min in the default conditions.Fig. 3.

Bottom Line: We develop an online tool, Cas-Database, a genome-wide gRNA library design tool for Cas9 nucleases from Streptococcus pyogenes (SpCas9).With an easy-to-use web interface, Cas-Database allows users to select optimal target sequences simply by changing the filtering conditions.Cas-Database also provides a web application programming interface (web API) for advanced bioinformatics users.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Hanyang University, Seoul 133-791, South Korea.

No MeSH data available.


Related in: MedlinePlus