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Team:LMU-Munich/Primer Design
From 2011.igem.org
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==Introduction== | ==Introduction== | ||
| - | + | Our aim with these tools is to assist the user with primer design for coding and non coding biobricks. In order to achieve this we chose two slightly different approaches for designing coding and noncoding biobricks. While only one input sequence is needed in order to design a coding biobrick we chose to use flanking regions of the sequence of a non doding biobrick. The reason herefor is that using flanking regions of a non coding sequence which is supposed to be amplified enables the possibility to create a broad range of primers which meet the necessary criteria for a working primer. | |
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| + | Hence we created ''Adjacent Regions'' and ''Design Primers''. | ||
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In case you find any bugs or have any comments, suggestions or questions please feel free to email us at | In case you find any bugs or have any comments, suggestions or questions please feel free to email us at | ||
Revision as of 22:53, 19 September 2011
Contents |
Introduction
Our aim with these tools is to assist the user with primer design for coding and non coding biobricks. In order to achieve this we chose two slightly different approaches for designing coding and noncoding biobricks. While only one input sequence is needed in order to design a coding biobrick we chose to use flanking regions of the sequence of a non doding biobrick. The reason herefor is that using flanking regions of a non coding sequence which is supposed to be amplified enables the possibility to create a broad range of primers which meet the necessary criteria for a working primer.
Hence we created Adjacent Regions and Design Primers.
In case you find any bugs or have any comments, suggestions or questions please feel free to email us at lmuprimer@googleemail.com
We provide two main functions and hope that these can help you during primer design.
Adjacent Regions
The main idea behind Adjacent Regions is that in case you would like to design a non coding Biobrick you can easily find adjacent regions of your Biobrick in the original host genome.
As options we provide the host genome as well as cutoff rates for the adjacent regions. The input would be the sequence of your Biobrick.
Click here to use this tool.
Design Primers
General Overview
Design Primers will provide you with several suggestions for primers and name soem of their properties which it determines. Only those primers are named which are not selfannealing and do not have a G or a C at the end of the sequence. Tm values are determined based on the Wallace Rule, potential Loop sites are named and the GC content of the annealing part of the primer is determined.
You will have to give either the Coding sequence of your Biobrick as an input in case you would like to create primers for a coding Biobrick or the flanking sequences of your Biobrick in case you would like to design a non codign Biobrick.
As options you can choose the length of the annealing part of the primers and the Biobrick format: Either the "classic" Biobrick or the Freiburg standard. You can also have your input sequences checked for restriction enzyme binding sites. Here you can choose whether to check for all known restriction enzymes, only those used in Biobricks or non at all.
Click here to use this tool.
How to interpret the results
You will be given a set of potential primers for both the forward primer as wells as the reverse primer. Next to the primer is the determined value of Tm. Next to the Tm value is the GC content. And as the very last value a potential Hairpin is being named. E.g. HAIRPIN?!7-4 would mean that there are 4 nucleotides at the very end of the sequence of the primer which might bind 4 other nucleotides after a loop of 7 nucleotides.
