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Parallel Overlap Assembly for DNA Libraries

Learn about the POA algorithm to construct computational DNA libraries efficiently. Explore examples and applications of the technique, including overlap sizes and error prevention.

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Parallel Overlap Assembly for 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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