Difference between revisions of "Part:BBa K1431402:Design"
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====Select gRNA sequences with the best theoretical quality====
 
====Select gRNA sequences with the best theoretical quality====
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===Source===
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AB010289-AB078031 in HBV_aligned Database
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===References===

Revision as of 03:41, 18 October 2014

gRNA1 for HBV


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Designing the Sequence

We used a method derived from the method described in the paper by Feng Zhang[http://www.nature.com/nbt/journal/v31/n9/abs/nbt.2647.html ZhangFgRNA].

The whole process can be divided into the following steps:

Conserved Sequence Analysis

We first extracted all conserved regions from the NIH HIV-1 Reference Genome. In this step, we found around 10 alternatives for the next process. Here all screening processes are done in a per-strain basis because of the high mutability of the HIV-1 virus.

Strip out sequences without PAM

Select gRNA sequences with the best theoretical quality

Source

AB010289-AB078031 in HBV_aligned Database

References