Lecture Notes 4.B

These oligonucleotides were then combined to form

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Unformatted text preview: nucleotides). by the 5’ 10-mer of the sequence representing vj . These oligonucleotides were then combined to form strands ¶3. encoding random paths through the graph. An (illegal) example path (v1 → with They were generated at random and assigned to the vertices, but vthe restriction depicted in Fig. them were too similar or complementary. 2 → v3 → v4 ) is that none of 5.4. Fixed amounts (50 pmol) of each oligonucleotide were mixed together in ¶4. aEach vertex code can At the end of this catenationis assumed that a vi = single ligation reaction. be considered a reaction, it of two 10mers: ai b i . (I.e., ai is the 50 10mer and bi is the 30 10mer.) ¶5. Edges: Also represented by 20mers. The edge from vertex i to vertex j is represented by ei!j = bi aj , where vi = ai bi , and vj = aj bj . 4 https://en.wikipedia.org/wiki/Adleman, Leonard (accessed 2012-11-04). B. FILTERING MODELS 233 ¶6. Paths: Paths are represented by using complements of the vertex 20mers to stitch together the edge 20mers. (Of course, using the complements of the edges to stitch together the vertices works as well.) For example, a path 2 ! 3 ! 4 is represented: e e z 2!3 { z 3!4 { }| }| b 2 a3 b 3 a4 a3 b 3 | {z } v3 ¶7. Initial and final edges: Edges from vin and to vout have special representations as 30mers: ein!j = vin aj , where vj = aj bj , ei!out = bi vout , where vi = ai bi . ¶8. Note that the special representation of the initial and terminal edges results in blunt ends for complete paths. ¶9. Therefore, for the n = 7 problems, candidate solutions were 140bp in length. There are n 1 edges, but the first and last edges are 30mers. He...
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