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On the complexity of positional sequencing by hybridization.
Summary
This study presents a fast algorithm for positional sequencing by hybridization (PSBH) when DNA substrings have limited placement options. However, PSBH becomes computationally difficult with more complex substring position constraints.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Sequencing by hybridization (SBH) reconstructs DNA from short substrings.
- Original SBH is not competitive with gel-based methods.
- Positional SBH (PSBH) enhances SBH with substring position information.
Purpose of the Study:
- To develop efficient algorithms for Positional SBH.
- To analyze the computational complexity of PSBH under varying constraints.
Main Methods:
- Developed a linear time algorithm for PSBH with at most two possible positions per substring.
- Proved NP-completeness for PSBH with at most three possible positions per substring.
- Investigated PSBH with interval-based position constraints.
Main Results:
- A linear time algorithm was achieved for a restricted PSBH case.
- PSBH was shown to be NP-complete for slightly more complex position constraints.
- A fast algorithm was provided for interval-based PSBH when interval length is bounded.
Conclusions:
- PSBH is efficient for specific, limited position information.
- The computational complexity of PSBH increases significantly with more flexible position constraints.
- Algorithmic solutions exist for PSBH with bounded interval position constraints.