"
Team:Washington/Outreach/iGEM Collaborations
From 2011.igem.org
(Difference between revisions)
| Line 2: | Line 2: | ||
__NOTOC__ | __NOTOC__ | ||
| - | <center><big><big><big><big>Community Outreach: iGEM Collaborations</big></big></big></big></center><br><br> | + | <center><big><big><big><big>'''Community Outreach: iGEM Collaborations'''</big></big></big></big></center><br><br> |
| - | =Primer Design Tool with LMU-Munich= | + | ='''Primer Design Tool with LMU-Munich'''= |
We worked with [https://2011.igem.org/Team:LMU-Munich LMU-Munich 2011] iGEM team this summer on the testing and development of their PrimerDesign tool. To learn more about it check out their [https://2011.igem.org/Team:LMU-Munich/Primer_Design/Design_Primers website]. | We worked with [https://2011.igem.org/Team:LMU-Munich LMU-Munich 2011] iGEM team this summer on the testing and development of their PrimerDesign tool. To learn more about it check out their [https://2011.igem.org/Team:LMU-Munich/Primer_Design/Design_Primers website]. | ||
| - | ==Software Testing== | + | =='''Software Testing'''== |
We helped LMU-Munich test their primer design software by sending our primer data and comparing it with the output of their automated designer. To do this, we compared the sequences of the primers used to amplify out parts of the LuxBrick with the primers that their software designed and concluded that their software works as expected. Unfortunately, we did not have enough time to order the primers that the software designed to test it ourselves. Overall, we found the tool easy to use and potentially very useful for future primer design. | We helped LMU-Munich test their primer design software by sending our primer data and comparing it with the output of their automated designer. To do this, we compared the sequences of the primers used to amplify out parts of the LuxBrick with the primers that their software designed and concluded that their software works as expected. Unfortunately, we did not have enough time to order the primers that the software designed to test it ourselves. Overall, we found the tool easy to use and potentially very useful for future primer design. | ||
| Line 14: | Line 14: | ||
[[File:Washington_collab_test.png|left|550px|thumb|An example of the output from the tool based off of input from our luxC biobrick, multiple primers with various melting temperatures are given]] | [[File:Washington_collab_test.png|left|550px|thumb|An example of the output from the tool based off of input from our luxC biobrick, multiple primers with various melting temperatures are given]] | ||
| - | ==Implemented Bug Fixes & Features== | + | =='''Implemented Bug Fixes & Features'''== |
#Added cyanobacteria to available genomes | #Added cyanobacteria to available genomes | ||
#Switch coding sequences in the primer designer to allow for the user to incude a stop codon in a coding sequence. Before, software insisted that coding sequences not include the stop codon | #Switch coding sequences in the primer designer to allow for the user to incude a stop codon in a coding sequence. Before, software insisted that coding sequences not include the stop codon | ||
Revision as of 02:39, 23 September 2011
Primer Design Tool with LMU-Munich
We worked with LMU-Munich 2011 iGEM team this summer on the testing and development of their PrimerDesign tool. To learn more about it check out their website.
Software Testing
We helped LMU-Munich test their primer design software by sending our primer data and comparing it with the output of their automated designer. To do this, we compared the sequences of the primers used to amplify out parts of the LuxBrick with the primers that their software designed and concluded that their software works as expected. Unfortunately, we did not have enough time to order the primers that the software designed to test it ourselves. Overall, we found the tool easy to use and potentially very useful for future primer design.
Implemented Bug Fixes & Features
- Added cyanobacteria to available genomes
- Switch coding sequences in the primer designer to allow for the user to incude a stop codon in a coding sequence. Before, software insisted that coding sequences not include the stop codon
- Made primer designer default to only check for biobrick restriction enzymes. Before, Primer Designer defaulted to checking for all restriction sites, making the user scroll to the bottom of the page for results
- added support for FASTA files with headers
- added desriptions for each column of the Primer Designer output.
