From 2014.igem.org

Revision as of 18:57, 17 October 2014

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. Homeoregion'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 homeoregions 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.

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  Design Principle

  Homeoregion:
     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)

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  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.

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  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.

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  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