"
Team:British Columbia/humanpractices/SpaceR
From 2013.igem.org
| (7 intermediate revisions not shown) | |||
| Line 17: | Line 17: | ||
<p> | <p> | ||
| - | In order to ensure that all possible off targets are listed, the blast search is optimized for short sequence mapping, excludes the PAM sequence, and gives | + | In order to ensure that all possible off targets are listed, the blast search is optimized for short sequence mapping, excludes the PAM sequence, and gives up to 500 top hits. All the databases are also kept in house for added efficiency and security. |
Here’s an example of what a blast output from our pipeline would look like: | Here’s an example of what a blast output from our pipeline would look like: | ||
</p> | </p> | ||
<center> | <center> | ||
| - | + | https://static.igem.org/mediawiki/2013/a/a2/Screen_Shot_2013-09-27_at_8.05.47_PM.png"> | |
</center> | </center> | ||
| - | + | ||
<p> | <p> | ||
| Line 31: | Line 31: | ||
<center> | <center> | ||
| - | + | https://static.igem.org/mediawiki/2013/4/41/Screen_Shot_2013-09-27_at_8.19.32_PM.png"> | |
</center> | </center> | ||
| - | + | ||
<p> | <p> | ||
We are currently setting up the infrastructure and logistics for the Space-R repository. We would greatly appreciate any feedback on the project! | We are currently setting up the infrastructure and logistics for the Space-R repository. We would greatly appreciate any feedback on the project! | ||
</p> | </p> | ||
| + | |||
| + | <br> | ||
| + | |||
| + | <html> | ||
| + | |||
| + | <div> | ||
| + | <center> | ||
| + | |||
| + | <a href="https://2013.igem.org/Team:British_Columbia/humanpractices"> | ||
| + | <img width="180px" class="icon" src="https://static.igem.org/mediawiki/2013/7/79/UBCReturnArrow.png" | ||
| + | onmouseover="this.src='https://static.igem.org/mediawiki/2013/1/11/UBCReturnHP.png'" | ||
| + | onmouseout="this.src='https://static.igem.org/mediawiki/2013/7/79/UBCReturnArrow.png'"/></a> | ||
| + | </center> | ||
| + | </div> | ||
| + | |||
| + | |||
| + | </html> | ||
Latest revision as of 03:41, 29 October 2013
iGEM Home
CRISPR Space-R
The CRISPR system gains it's specificity through RNA transcribed from highly variable spacer regions that are separated by conserved repeat regions. The resulting small RNAs are used to target phage DNA and confer immunity to the bacterial host. While one of the most useful feature of CRISPR is it's easily engineered specificity, spacer regions could potentially have "off target" activity and unintended implications. We are currently in the process of building a repository for CRISPR spacer sequences for the iGEM community. Our server will host the sequences and a BLAST-pipeline that will retrieve all the possible sequences from public databases that could be targeted by the submitted spacer. Once a spacer sequence is submitted and BLAST-results are generated, a review process will take place where two anonymous iGEM teams submit a safety assessment. This will include possible societal, environmental and scientific implications of the spacer region as they relate to the possible target sequences. Moreover, this could help seed new ideas and applications with the newly designed spacers. Here is an example of a submission form for Space-R:
In order to ensure that all possible off targets are listed, the blast search is optimized for short sequence mapping, excludes the PAM sequence, and gives up to 500 top hits. All the databases are also kept in house for added efficiency and security. Here’s an example of what a blast output from our pipeline would look like:
">
From this, the results would be sent out with a review form that would be filled in by anonymous iGEM teams. Here’s an example:
">
We are currently setting up the infrastructure and logistics for the Space-R repository. We would greatly appreciate any feedback on the project!
