Paul A. Gagniuc - Algorithms in Bioinformatics

16 Chapter 17Table 17.1 A link between entropy, information, patterns, and the perception of ...

1 Chapter 1 Figure 1.1 The tree of life – basic diagram. The prebiotic period shown o... Figure 1.2 Ultrastructural images of adipocyte cells from Bos taurus (Ca... Figure 1.3 Molecular representations. (a) Shows the structure of the nuc...

2 Chapter 2 Figure 2.1 The average genome size. (a) Shows the proportion of known species i...

3 Chapter 3 Figure 3.1 Initialization of the score matrix.(a) Shows the values of the para... Figure 3.2 Traceback rules.(a) shows the link between the implementation and t...Figure 3.3 Additions and new possibilities for local sequence alignment.(a) It...

4 Chapter 4Figure 4.1 Local alignment regime and symbols.(a) A higher resolution of the h...Figure 4.2 True randomness and chaos. (a) Shows a series of heatmaps from exper...Figure 4.3 Alignment parameters and the significance of islands.(a–h) Indicate...Figure 4.4 A score matrix dissection through specially constructed sequences.E...Figure 4.5 BioJupiter interface and functionalities.(a–c) The application inte...

5 Chapter 5Figure 5.1 Self-sequence alignment – implementation vs. model.The ...

6 Chapter 6Figure 6.1 CpG% and the epigenetic programming.The top of the figure shows a h...

7 Chapter 7Figure 7.1 The objective digital stain method.(a) Shows the promoter sequence ...Figure 7.2 Examples of ODSs.(a) Shows an approach to the ODS analysis using a ...Figure 7.3 The ODS reference system.(a) Shows the standard reference system di...

8 Chapter 8Figure 8.1 Transcription, alternative splicing, and translation.It show...

9 Chapter 9Figure 9.1 Schematic representation of the PSSM.(a) Shows the principle behind...

10 Chapter 10Figure 10.1 A diagram of the scanning process.(a) Shows the contents of the fi...

11 Chapter 12Figure 12.1 Dynamic PWMs.(a) Shows the motif set and the transformation of thi...Figure 12.2 Merging a null model into the existing background PFM.(a) Shows th...Figure 12.3 Dynamic PWMs with real additions to the background set.The example...

12 Chapter 13Figure 13.1 Computation of transition matrices.(a) Shows the types of transiti...Figure 13.2 A Markov Chain experiment.(a) The probability values present insid...Figure 13.3 The Markov chains generator.The principle of operation of a Markov...

13 Chapter 14Figure 14.1 The log-likelihood matrix.(a) The panel shows sequence s0 , t...Figure 14.2 Local score computation by using the LLM.(a–c) The three panels sh...Figure 14.3 An experiment for understanding scores.(a) Shows the contents of t...

14 Chapter 15Figure 15.1 A graphical representation of the spectral forecast equation...Figure 15.2 Experimental predictions using the spectral forecast model. (a) Sig...

15 Chapter 17Figure 17.1 Limits of prediction, chaos, and noise. Each graph shows the evolut...

1 Cover Page

2 Title Page Algorithms in Bioinformatics Theory and Implementation Paul A. Gagniuc University Politehnica of Bucharest Bucharest, Romania

3 Copyright

4 Preface

5 About the Companion Website

6 Table of Contents

7 Begin Reading

8 Appendix A

9 References

10 Index

11 WILEY END USER LICENSE AGREEMENT

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