The fragment assembly string graph
Bioinformatics
Computability of models for sequence assembly
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
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Sequence assembly from short reads is an important problem in biology. It is known that solving the sequence assembly problem exactly on a bi-directed de Bruijn graph or a string graph is intractable. However finding a Shortest Double stranded DNA string (SDDNA) containing all the k-long words in the reads seems to be a good heuristic to get close to the original genome. This problem is equivalent to finding a cyclic Chinese Postman (CP) walk on the underlying unweighted bi-directed de Bruijn graph built from the reads. The Chinese Postman walk Problem (CPP) is solved by reducing it to a general bi-directed flow on this graph which runs in O(|E|2 log2(|V|)) time. In this paper we show that the cyclic CPP on bi-directed graphs can be solved without reducing it to bi-directed flow. We present a Θ(p(|V|+|E|) log(|V|)+(dmaxp)3) time algorithm to solve the cyclic CPP on a weighted bi-directed de Bruijn graph, where p = max{|{v|din(v) - dout(v) 0}|,|{v|din(v) - dout(v) dmax = max{|din(v) - dout(v)}. Our algorithm performs asymptotically better than the bi-directed flow algorithm when the number of imbalanced nodes p is much less than the nodes in the bi-directed graph. From our experimental results on various datasets, we have noticed that the value of p/|V| lies between 0.08% and 0.13% with 95% probability. Many practical bi-directed de Bruijn graphs do not have cyclic CP walks. In such cases it is not clear how the bi-directed flow can be useful in identifying contigs. Our algorithm can handle such situations and identify maximal bi-directed sub-graphs that have CP walks. We also present a Θ((|V| + |E|) log(V)) time algorithm for the single source shortest path problem on bi-directed de Bruijn graphs, which may be of independent interest.