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Table of contents
1 Introduction
1.1 Background
1.2 Challenges of detecting remote protein homology
1.3 Significance and contribution of the thesis
1.4 Publications
1.5 Organization of the thesis
List of Figures
List of Tables
2 Proteins
2.1 Structure and function
2.2 Homologous proteins
2.2.1 Remote homologous proteins
2.3 Protein families, domains and motifs
3 Methods for remote homology detection
3.1 Sequence Similarity Searching
3.2 Generative methods
3.2.1 Position-Specific Iterative BLAST
3.2.2 Profile Hidden Markov Models
3.2.3 Methods based on domain co-occurrence
3.3 Discriminative methods
3.3.1 Support vector machine
3.3.2 Inductive logic programming
3.4 Comparing different methods
4 ILP-SVM Homology
4.1 Background
4.2 Methods
4.2.1 Dataset description
4.2.2 Logical representations
4.2.3 Construction of propositional classifiers
4.2.4 Comparison between different methods
4.2.5 Parameter settings and tools used
4.3 Results and Discussion
4.4 Conclusion
5 CASH – Combination of Annotations by Species and pHMMs
5.1 Background
5.2 Methods
5.2.1 Databases
5.2.2 Selection of representative species from the eukaryotic tree of life
5.2.3 Pfam methodology
5.2.4 Phylogenetic Models
5.2.5 Combining Models Predictions
5.2.6 Resolving protein domain architectures
5.2.7 Prediction analysis
5.2.8 Comparison with earlier results
5.2.9 Visualizing our results
5.2.10 Parameter settings and tools used
5.3 Results and Discussion
5.4 Conclusion
6 General conclusions and future work
A List of representative species used in CASH system
B List of Pfam Ribosomal families
C Domains and architectures over-represented in P. falciparum
Bibliography
