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Parallel Overlap Assembly for the Construction Of Computational DNA Libraries

Parallel Overlap Assembly for the Construction Of Computational DNA Libraries. Presented by Nayeong Jeong. Introduction POA algorithm Example and application of POA Overlap size Conclusion. Introduction. What is POA ? P arallel O verlap A ssembly.

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Parallel Overlap Assembly for the Construction Of Computational DNA Libraries

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  1. Parallel Overlap Assembly for the Construction Of Computational DNA Libraries Presented byNayeong Jeong • Introduction • POA algorithm • Example and application of POA • Overlap size • Conclusion

  2. Introduction • What is POA ? • Parallel Overlap Assembly. • Algorithm to construct a DNA pool of molecules • with initially ordered data. • 2. How can we get ordered data? • Mix a bunch of oligonucleotides with primer known • already. Cycle in proper temperature then we • can get a diluted data. Repeat these steps with different • chemical liquid and temperature.

  3. Old Algorithm Match the sequence with specified characters like TGCA. POA Algorithm Change the character set with 16 binary numbers. Need two parameter : digit position(n) and its value(v). Let P(n) be a position string. V(nv) be a vlaue string. The fragments are constructed as following: P(n)V(nv)P(n+1) for even power of 2. P(n+1)V(nv)P(n) for odd power of 2.

  4. Example 1 0 1 1 5’ P(0)V(01)P(1) P(2)V(20)P(3) 3’ 3’ P(1)V(11)P(2) P(3)V(31)P(4) 5’ See Fig 2. => P(2)V(21)P(3)V(30)P(4)

  5. Fig1. Assembly numbers

  6. Fig2. Technique of POA

  7. Application of POA See Table 1. There are 10 data. It needs 4 stages to get the whole sequence in POA. But in sequential process, it needs 9 steps to get the same answer. Generally, Sequential program needs L/n steps. Parallel program needs slightly more than ln( L/n) steps. where L is sequence size. n is overlap size.

  8. Overlap size To reach the next step, the nucleotides of length n overlap by some number of base l. If l is not long enough, a nucleo- tides can match any other. Avoiding Errors. Make long base l. probability to find overlap in a sequence of L with m base. with gaps probability is

  9. Conclusion We can build combinational libraries with ordered sequence by extension, annealing, and melting. We can avoid error by reducing a mismatch annealing and extension. In order to do that overlap size should be big enough according to the following equation.

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