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Team:ZJU-China/Tools
From 2014.igem.org
| Team Sponsor | Contact us | ||
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Team Forum(BBS): | ZJU-China 2014 Team Forum on www.zjubiolab.zju.edu.cn | |
| Post Address: | Biolab Center Room 413, ZJU Zijin'gang Campus, Yuhang Tang Road No.866, Hangzhou, Zhejiang |
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| Powered by Media Wiki. Zhejiang University. | Email Address: | zjuchina2014 @ 163.com | |
GS-Box
A simple & efficient bioinformatics tool for Gene-Socket
Every excellent technique should be simple and efficient to use! As an excellent technique, gene-socket also does well in this respect------ it has its' own optimization tool: GS-BOX. GS-BOX is a bioinformatics tool which is designed for customs to build their own gen-sockets easily and efficiently. What need the customs do with the tool? Just input the gene circuit sequences and then GS-BOX will design the experimental process automatically and every detail that customs will need to use!
Service
GS-Box provides 3 kinds of modes and 7 services.
For mode 1, GS-Box can provide:
i. Homoedomain's sequence
ii. P-primer's sequence
iii. P-primer's GC percent
iv. P-primer's TM value
v. F-primer's sequence
vi. F-primer GC percent
vii. F-primer TM value
For other modes, it cotains two homoedomains and also two P-primers and F-primers.
If you dont know how to use these sources, please read the example below or read our projectcarefully.
Design Principle
Homeodomains:
1. Don't have similar sequences with E.coli
(to avoid off-target effects)
2. Don't have similar sequences with custom's parts
(to avoid off-target effects)
3. Fit the subsequent steps' requiring
Primer:
1. GC content & TM value
(to ensure that PCR can work. If the GC percent is between 40% -60%, the PCR result will be fine)
2. Duplex formation and hairpin
(to ensure that PCR can work. If the primer has duplex formation and hairpin, the PCR cannot get result)
3. Proper length
(to ensure that PCR can work. If the length is too short, the PCR cannot get the result; If the length is too long, the TM value will be very high and make PCR's result not good)
Design Method
Step 1. Generate more than 1000 sequences which contains 40 bp and are made of A/T/G/C
Step 2. Do blast between the sequences and the E.coli's genome to delete some sequences which have samilar sequences with E.coli. As a result, a database which has 1000 sequences was established.
Step 3. Do blast between the custom's sequences and the database's data to delete some sequences which have samilar sequences with custom's sequences. As a result, a secondary database was established.
Step 4. Select some data in the secondary database which has proper primer.
Step 5. Print out the primer's information.
How to use
GS-Box has 3 modes.
If you want to build a circuit which doesn't contian a promoter or terminator inside the circuit, you shuld choose mode 1;
If you want to build a circuit which contians a promoter but not a terminator inside the circuit, you shuld choose mode 2;
If you want to build a circuit which contians a terminator but not a promoter inside the circuit, you shuld choose mode 3;
For more information, please see the solution below.
Help
You should know that if you choose a mode, this mode will be used for all of your parts. So if you just want to use the special mode for only one of your parts, you should use GS-Box twice, once without the special part and once only contain the special part.
For more information, please see the example below.
If you still have any questions when using GS-Box, please contact us.
Team Forum(BBS):
ZJU-China 2014 Team Forum on ZJU Sever
Post Address:
Biolab Center Room 413, ZJU Zijin'gang Campus, Yuhang Tang Road No.866, Hangzhou, Zhejiang
Email Address:
zjuchina2014 @ 163.com
Solution
Watch this viedo, and this will help you understand what Gene-Socket did and what GS-Box's four modes mean
imagine here is a video
As you see, If you want to use GS-Box to insert your part into the chromosome, you don't need to submit the promoter and terminator because ZJU-CHINA2014 had built it already for you. But if your promoter or terminator is special and you have to use it rather than using the official promoter or terminator, you need to think of your situations. There exists 3 situaitions:
- Mode 1: You choose to use the official promoter & terminator
- Mode 2: Your part contains a promoter and you want to use it
- Mode 3: Your part contains a terminator
Mode 1:
If you want to build a circuit which has one promoter, one fuction gene and one terminator, you just need to submit the fuction gene because GS-Box has designed the promoter and terminator already. That is, you can regard the fuction gene as a "part". Now you need to insert the "part" into the device on chromosome. It is easy to achieve this goal if you use Gene-Socket, but before you use it you need to modify your "part" just like the picture below. This is the mode 1.
Mode 2:
What if you want to build this one --- a circuit with a special promoter that you need to use. In this case, you can modify your "part" in a different way and can work normal. This kind of modification is established just like the picture showed. This is the mode 2.
Mode 3:
If you have a circuit which must contian a terminator inside the circuit, as you see, the Gene-Socket will not work. What should you do on this occasion? You can modify your "part" in a different way, that is, add a promoter behind the part and as a result the problem will be solved. The way you modify your "part" is just like the picture showed. This is the mode 3.
Example
Example 1:
I just want to insert a simple gene---GFP(see the picture below). This situation is very simple. According to "How to Use GS-Box", this is the mode 1, and I need to modify it as the picture below.
Example 2:
I want to insert a circuit, which contains a promoter, a RBS and GFP(see the picture below). According to "How to Use GS-Box", this is the mode 2, and I need to modify it as the picture below.
Example 3:
I want to insert a circuit which contains a RBS, a GFP and a terminator(see the picture below). According to "How to Use GS-Box", this is the mode 3, and I need to modify it as the picture below.
