On the Complexity of Positional Sequencing by Hybridization

In sequencing by hybridization (SBH), one has to reconstruct a sequence from its l-long substrings. SBH was proposed as an alternative to gel-based DNA sequencing approaches, but in its original form the method is not competitive. Positional SBH (PSBH) is a recently proposed enhancement of SBH in which one has additional information about the possible positions of each substring along the target sequence. We give a linear time algorithm for solving PSBH when each substring has at most two possible positions. On the other hand, we prove that the problem is NP-complete if each substring has at most three possible positions. We also show that PSBH is NP-complete if the set of allowed positions for each substring is an interval of length k, and provide a fast algorithm for the latter problem when k is bounded. Key Words: Positional Sequencing by Hybridization, Complexity, Eulerian Graphs, NP-Hardness, Parameterized Algorithms. 1 Introduction Sequencing by hybridization (SBH) was proposed ..

Modern genome annotation: The BioSapiens network

In order to maximise our understanding of biology and evolution, gained from the large scale sequencing projects of the current era, it is necessary to be able to assign detailed biochemical, cellular and developmental functions to as many protein sequences as possible. More than five million distinct proteins can be found in the major public repositories, i.e., UniProt & RefSeq (Pruitt et al. 2007; UniProt Consortium 2007), but detailed laboratory investigations have only been carried out for a tiny fraction. For instance, only ~ 25,000 proteins have solved structures in the international protein structure repository, the worldwide Protein Data Bank (wwPDB, Berman et al. 2003)