Genome Clustering

1. Front Matter

   PDF

2. Biological Background

   • Alexander Bolshoy, Zeev (Vladimir) Volkovich, Valery Kirzhner, Zeev Barzily

   Pages 1-16

3. Biological Classification

   • Alexander Bolshoy, Zeev (Vladimir) Volkovich, Valery Kirzhner, Zeev Barzily

   Pages 17-22

4. Mathematical Models for the Analysis of Natural-Language Documents

   • Alexander Bolshoy, Zeev (Vladimir) Volkovich, Valery Kirzhner, Zeev Barzily

   Pages 23-42

5. DNA Texts

   • Alexander Bolshoy, Zeev (Vladimir) Volkovich, Valery Kirzhner, Zeev Barzily

   Pages 43-60

6. N-Gram Spectra of the DNA Text

   • Alexander Bolshoy, Zeev (Vladimir) Volkovich, Valery Kirzhner, Zeev Barzily

   Pages 61-85

7. Application of Compositional Spectra to DNA Sequences

   • Alexander Bolshoy, Zeev (Vladimir) Volkovich, Valery Kirzhner, Zeev Barzily

   Pages 87-112

8. Marker-Function Profile-Based Clustering

   • Alexander Bolshoy, Zeev (Vladimir) Volkovich, Valery Kirzhner, Zeev Barzily

   Pages 113-145

9. Genome as a Bag of Genes – The Whole-Genome Phylogenetics

   • Alexander Bolshoy, Zeev (Vladimir) Volkovich, Valery Kirzhner, Zeev Barzily

   Pages 147-160

10. Back Matter

    PDF

Knighting in sequence biology Edward N. Trifonov Genome classification, construction of phylogenetic trees, became today a major approach in studying evolutionary relatedness of various species in their vast - versity. Although the modern genome clustering delivers the trees which are very similar to those generated by classical means, and basic terminology is the same, the phenotypic traits and habitats are not anymore the playground for the classi- cation. The sequence space is the playground now. The phenotypic traits are - placed by sequence characteristics, “words”, in particular. Matter-of-factually, the phenotype and genotype merged, to confusion of both classical and modern p- logeneticists. Accordingly, a completely new vocabulary of stringology, information theory and applied mathematics took over. And a new brand of scientists emerged – those who do know the math and, simultaneously, (do?) know biology. The book is written by the authors of this new brand. There is no way to test their literacy in biology, as no biologist by training would even try to enter into the elite circle of those who masters their almost occult language. But the army of - formaticians, formal linguists, mathematicians humbly (or aggressively) longing to join modern biology, got an excellent introduction to the field of genome cl- tering, written by the team of their kin.

• Bioinformatics
• Computational Intelligence
• General Spectum Approach
• classification
• genetics
• genome

• The Department of Evolutionary and Environmental Biology and the Institute of Evolution, University of Haifa, Haifa, Israel

  Alexander Bolshoy

• Software Engineering Department, ORT Braude College, Karmiel, Israel

  Zeev (Vladimir) Volkovich, Zeev Barzily

• The Institute of Evolution, University of Haifa, Haifa, Israel

  Valery Kirzhner

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