Bioinformatics of Genome Regulation and Structure II

Front Matter....Pages 1-1
Recognition of Coding Regions in Genome Alignment....Pages 3-10
Predicting sRNA Genes in the Genome of E. Coli by the Promoter-Search Algorithm PlatProm....Pages 11-20
Content Sensors Based on Codon Structure and DNA Methylation for Gene Finding in Vertebrate Genomes....Pages 21-29
The Sitega Tool for Recognition and Context Analysis of Transcription Factor Binding Sites: Significant Dinucleotide Features Besides the Canonical Consensus Exemplified By SF-1 Binding Site....Pages 31-41
Transcription Regulatory Regions Database (TRRD): A Source of Experimentally Confirmed Data on Transcription Regulatory Regions of Eukaryotic Genes....Pages 43-53
Artsite Database: Comparison of In Vitro Selected and Natural Binding Sites of Eukaryotic Transcription Factors....Pages 55-65
Comparative Analysis of Electrostatic Patterns for Promoter and Nonpromoter DNA in E. Coli Genome....Pages 67-74
Analysis of Nucleosome Formation Potential and Conformational Properties of Human J1-J2 and D2-D1 Type Alpha Satellite DNA....Pages 75-83
VMM: A Variable Memory Markov Model Prediction of Nucleosome Formation Sites....Pages 85-95
DNA Nucleosome Organization of the Promoter Gene Regions....Pages 97-103
A Toolbox for Analysis of RNA Secondary Structure Based on Genetic Algorithm....Pages 105-110
Comparative Genomics and Evolution of Bacterial Regulatory Systems....Pages 111-119
Comparative Whole Genome Sequence Analysis of Corynebacteria....Pages 121-129
New LTR Retrotransposable Elements from Eukaryotic Genomes....Pages 131-140
A Genome-Wide Identification of Mitochondrial DNA Topoisomerase I in Arabidopsis ....Pages 141-145
Change in CpG Context is a Leading Cause of Correlation between the Rates of Non-Synonymous and Synonymous Substitutions in Rodents....Pages 147-151
Universal Seven-Cluster Structure of Genome Fragment Distribution: Basic Symmetry in Triplet Frequencies....Pages 153-163
New Methods to Infer DNA Function from Sequence Information....Pages 165-177
Revelation and Classification of Dinucleotide Periodicity of Bacterial Genomes Using the Method of Information Decomposition....Pages 179-188
Algorithms to Reconstruct Evolutionary Events at Molecular Level and Infer Species Phylogeny....Pages 189-204
Front Matter....Pages 205-205
Mining from Complete Proteomes to Identify Adhesins and Adhesin-Like Proteins: A Rapid Aid to Experimental Researchers....Pages 207-214
Central Moments Based Statistical Analysis for the Determination of Functional Sites in Proteins with Thematics....Pages 215-224
Amino Acids Surface Patterns in Protein Domain Functionality Analysis....Pages 225-233
Computer Simulations of Anionic Unsaturated Lipid Bilayer—A Suitable Model to Study Membrane Interactions with A Cell-Penetrating Peptide....Pages 235-246
The Role of Water in Homeodomain-DNA Interaction....Pages 247-257
Molecular Modeling of Human MT 1 and MT 2 Melatonin Receptors....Pages 259-270
Molecular Dynamics of Small Peptides Using Ergodic Trajectories....Pages 271-284
A Periodical Nature of 94 Protein Families....Pages 285-295
Prediction of Contact Numbers of Amino Acid Residues Using a Neural Network Model....Pages 297-304
Fastprot: A Computational Workbench for Recognition of the Structural and Functional Determinants in Protein Tertiary Structures....Pages 305-316
A Markov Model for Protein Sequences....Pages 317-327
Proteome Complexity Measures Based on Counting of Domain-to-Protein Links for Replicative and Non-Replicative Domains....Pages 329-341
Front Matter....Pages 343-343
A Software Architecture for Developmental Modeling in Plants: The Computable Plant Project....Pages 345-354
Prediction and Alignment of Metabolic Pathways....Pages 355-365
General Principles of Organization and Laws of Functioning in Governing Gene Networks....Pages 367-377
From Gradients to Stripes: A Logical Analysis of Drosophila Segmentation Genetic Network....Pages 379-390
Self-Oscillations in Hypothetical Gene Networks....Pages 391-404
Periodic Trajectories and Andronov-Hopf Bifurcations in Models of Gene Networks....Pages 405-414
On the Problem of Search for Stationary Points in Regulatory Circuits of Gene Networks....Pages 415-420
Modeling of Gene Expression by the Delay Equation....Pages 421-431
Front Matter....Pages 343-343
AGNS—A Database on Expression of Arabidopsis Genes....Pages 433-442
Study of the Interactions between Viral and Human Genomes During Transformation of B Cells with Epstein-Barr Virus....Pages 443-450
Probing Gene Expression: Sequence-Specific Hybridization on Microarrays....Pages 451-466
Determination of the Developmental Age of a Drosophila Embryo from Confocal Images of its Segmentation Gene Expression Patterns....Pages 467-478
Front Matter....Pages 479-479
Topical Clustering of Biomedical Abstracts by Self-Organizing Maps....Pages 481-490
Software for Analysis of Gene Regulatory Sequences by Knowledge Discovery Methods....Pages 491-498
A Mathematical Model of the Discontinuous Genetic Structures Fixation Process....Pages 499-509