Tutorial Activity 5

# Tutorial Activity 5 - MH 8300 Tutorial Activity 5 De Bruijn...

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MH 8300 Tutorial Activity 5 De Bruijn Graphs and Sequence Assembly Set A Group Members Name NTU Email ID Marks : /2

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MH 8300 Tutorial Activity 5 De Bruijn Graphs and Sequence Assembly Set A Question 1. Suppose we have a circular sequence of length 14 over the alphabet { A , T , C , G } . We obtain the following 14 fragments of length three , X = { AAT , ATA , ATT , ATC , ATG , TAT , TTC , TCA , TCG , TGA , CAT , CGA , GAA , GAT } . (a) Construct the de Bruijn graph based on the set of fragments X . (b) For each vertex, write down its in-degree and out-degree. (c) Based on (b), explain why the graph has an Eulerian circuit.
(d) What is the maximum out-degree amongst all its vertices? (e) Explain why the out-degree of any vertex in any de Bruijn graph (based on fragments from a { A , T , C , G } -sequence) cannot be bigger than four. (f) Construct an Eulerian circuit on the graph given in (a). (g) What is a possible circular sequence that gives the set of fragments X ?

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Question 2. Suppose we have a circular sequence of length 14 over the alphabet { A , T , C , G } . We obtain the following 14 fragments of length eight , Y = { AATATCAT , ATATCATG , ATTCGAAT , ATCATGAT , ATGATTCG ,
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