Genome Assemby, Chinese Postman, and Virtual Clusters

Google Tech Talk May 11, 2007 ABSTRACT In the first half of the talk I will discuss several algorithmic results affecting whole genome assembly -- the problem of assembling a genome from short pieces (called reads). This problem is often reduced to various path problems on graphs. We will first show that the problem of finding the Shortest Chinese Superwalk on a de Bruijn graph is NP-complete/hard, hence demonstrating the computational equivalence of two methods for sequenceassembly: the String Graph approach of Myers et al and the Eulerian Superpath approach of Pevzner et al. We will also demonstrate a simple polynomial time algorithm separating complimentary paths on a graph, which is...