Sequencing-by-Hybridization at the Information-Theory Bound: An Optimal Algorithm

Optimal Probing Patterns for Sequencing by Hybridization

Sequencing by Hybridization (SBH) is a method for reconstructing a DNA sequence based on its k-mer content. This content, called the spectrum of the sequence, can be obtained from hybridization with a universal DNA chip. The main shortcoming of SBH is that it reliably reconstructs only sequences of length at most square root of the size of the chip. Frieze et al. [9] showed that by using gapped...

Optimal Sequencing By Hybridization in Rounds

Positional sequencing by hybridization

Sequencing by hybridization (SBH) is a promising alternative to the classical DNA sequencing approaches. However, the resolving power of SBH is rather low: with 64kb sequencing chips, unknown DNA fragments only as long as 200 bp can be reconstructed in a single SBH experiment. To improve the resolving power of SBH, positional SBH (PSBH) has recently been suggested; this allows (with additional ...

Optimal Detection of Oil Contamination at Sea by the FPSO Algorithm

Leakage of oil from pipelines and oil tankers into seas and oceans is ecologically important and can have significant social and economic impacts on the environment. An early detection of deliberate or accidental oil spills can reduce serious hazards that may threaten coastal residents and help identify pollutants. Iran has been surrounded by seas from the north and the south and they provide u...

An Improved Branch and Bound Algorithm for Cyclopeptide Sequencing

15 Abstract— The mass-production of antibiotics and medication has started an evolutionary race between antibiotics and bacteria. Pharmaceutical companies proved helpful to create new antibiotics, while pathogens developed a new level of resistance to these antibiotics. Growth of drug-resistant disease increases the challenge of searching for new, more effective antibiotics. The isolation and s...