Metaheuristics for String Problems in Bio-informatics

Table of contents

1. Cover
2. Dedication
3. Title
4. Copyright
5. Preface
6. Acknowledgments
7. List of Acronyms
8. 1 Introduction
   1. 1.1. Complete methods for combinatorial optimization
   2. 1.2. Approximate methods: metaheuristics
   3. 1.3. Outline of the book
9. 2 Minimum Common String Partition Problem
   1. 2.1. The MCSP problem
   2. 2.2. An ILP model for the UMCSP problem
   3. 2.3. Greedy approach
   4. 2.4. Construct, merge, solve and adapt
   5. 2.5. Experimental evaluation
   6. 2.6. Future work
10. 3 Longest Common Subsequence Problems
    1. 3.1. Introduction
    2. 3.2. Algorithms for the LCS problem
    3. 3.3. Algorithms for the RFLCS problem
    4. 3.4. Future work
11. 4 The Most Strings With Few Bad Columns Problem
    1. 4.1. The MSFBC problem
    2. 4.2. An ILP model for the MSFBC problem
    3. 4.3. Heuristic approaches
    4. 4.4. ILP-based large neighborhood search
    5. 4.5. Experimental evaluation
    6. 4.6. Future work
12. 5 Consensus String Problems
    1. 5.1. Introduction
    2. 5.2. Organization of this chapter
    3. 5.3. The closest string problem and the close to most string problem
    4. 5.4. The farthest string problem and the far from most string problem
    5. 5.5. An ILP-based heuristic
    6. 5.6. Future work
13. 6 Alignment Problems
    1. 6.1. Introduction
    2. 6.2. The pairwise alignment problem
    3. 6.3. The multiple alignment problem
    4. 6.4. Conclusion and future work
14. 7 Conclusions
    1. 7.1. DNA sequencing
    2. 7.2. Founder sequence reconstruction
    3. 7.3. Final remarks
15. Bibliography
16. Index
17. End User License Agreement