Reconstructing Strings from Substrings in Rounds

We establish a variety of combinatorial bounds on the tradeo s inherent in reconstructing strings using few rounds of a given number of substring queries per round. These results lead us to propose a new approach to sequencing by hybridization (SBH), which uses interaction to dramatically reduce the number of oligonucleotides used for de novo sequencing of large DNA fragments, while preserving the parallelism which is the primary advantage of SBH.

• Type: Conference
• Year: 1995
• Where: FOCS
• Authors: Dimitris Margaritis, Steven Skiena
• Keywords: Combinatorial Bounds, FOCS 1995, Large Dna Fragments, Sequencing, Theoretical Computer Science