Reconstructing strings from substrings in rounds
Dimosthenis Margaritis, Steven Skiena · 2002
We establish a variety of combinatorial bounds on the tradeoffs 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.