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Bioinformatics of genome regulation and structure II / edited by Nikolay Kolchanov, Ralf Hofestaedt, Luciano Milanesi. — New York : Springer, c2006.—(58.174252/B615b) |
Contents
CONTENTS
PART 1. COMPUTATIONAL STRUCTURAL， FUNCTIONAL AND EVOLUTIONARY GENOMICS 1
RECOGNITION OF CODING REGIONS IN GENOME ALIGNMENT 3
PREDICTING sRNA GENES IN THE GENOME OF E. COLI BY THE PROMOTER-SEARCH ALGORITHM PlatProm 11
CONTENT SENSORS BASED ON CODON STRUCTURE AND DNA METHYLATION FOR GENIE FINDING IN VERTEBRATE GENOMES 21
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 31
TRANSCRIPTION REGULATORY REGIONS DATABASE (TRRD): A SOURCE OF EXPERIMENTALLY CONFIRMED DATA ON TRANSCRIPTION REGULATORY REGIONS OF EUKARYOTIC GENES 43
ARTSITE DATABASE: COMPARISON OF IN VITRO SELECTED AND NATURAL BINDING SITES OF EUKARYOTIC TRANSCRIPTION FACTORS 55
COMPARATIVE ANALYSIS OF ELECTROSTATIC PATTERNS FOR PROMOTER AND NONPROMOTER DNA IN E. COLI GENOME 67
ANALYSIS OF NUCLEOSOME FORMATION POTENTIAL AND CONFORMATIONAL PROPERTIES OF HUMAN J1-J2 AND D2-D1 TYPE ALPHA SATELLITE DNA 75
VMM: A VARIABLE MEMORY MARKOV MODEL PREDICTION OF NUCLEOSOME FORMATION SITES 85
DNA NUCLEOSOME ORGANIZATION OF THE PROMOTER GENE REGIONS 97
A TOOLBOX FOR ANALYSIS OF RNA SECONDARY STRUCTURE BASED ON GENETIC ALGORITHM 105
COMPARATIVE GENOMICS AND EVOLUTION OF BACTERIAL REGULATORY SYSTEMS 111
COMPARATIVE WHOLE GENOME SEQUENCE ANALYSIS OF CORYNEBACTERIA 121
NEW LTR RETROTRANSPOSABLE ELEMENTS FROM EUKARYOTIC GENOMES 131
A GENOME-WIDE IDENTIFICATION OF MITOCHONDRIAL DNA TOPOISOMERASE I IN ARABIDOPSIS 141
CHANGE IN CpG CONTEXT IS A LEADING CAUSE OF CORRELATION BETWEEN THE RATES OF NON-SYNONYMOUS AND SYNONYMOUS SUBSTITUTIONS IN RODENTS 147
UNIVERSAL SEVEN-CLUSTER STRUCTURE OF GENOME FRAGMENT DISTRIBUTION: BASIC SYMMETRY IN TRIPLET FREQUENCIES 153
NEW METHODS TO INFER DNA FUNCTION FROM SEQUENCE INFORMATION 165
REVELATION AND CLASSIFICATION OF DINUCLEOTIDE PERIODICITY OF BACTERIAL GENOMES USING THE METHOD OF INFORMATION DECOMPOSITION 179
ALGORITHMS TO RECONSTRUCT EVOLUTIONARY EVENTS AT MOLECULAR LEVEL AND INFER SPECIES PHYLOGENY 189
PART 2. COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS 205
MINING FROM COMPLETE PROTEOMES TO IDENTIFY ADHESINS AND ADHESIN-LIKE PROTEINS: A RAPID AID TO EXPERIMENTAL RESEARCHERS 207
CENTRAL MOMENTS BASED STATISTICAL ANALYSIS FOR THE DETERMINATION OF FUNCTIONAL SITES IN PROTEINS WITH THEMATICS 215
AMINO ACIDS SURFACE PATTERNS IN PROTEIN DOMAIN FUNCTIONALITY ANALYSIS 225
COMPUTER SIMULATIONS OF ANIONIC UNSATURATED LIPID BILAYER--A SUITABLE MODEL TO STUDY MEMBRANE INTERACTIONS WITH A CELL-PENETRATING PEPTIDE 235
THE ROLE OF WATER IN HOMEODOMAIN-DNA INTERACTION 247
MOLECULAR MODELING OF HUMAN MT1 AND MT2 MELATONIN RECEPTORS 259
MOLECULAR DYNAMICS OF SMALL PEPTIDES USING ERGODIC TRAJECTORIES 271
A PERIODICAL NATURE OF 94 PROTEIN FAMILIES 285
PREDICTION OF CONTACT NUMBERS OF AMINO ACID RESIDUES USING A NEURAL NETWORK MODEL 297
FASTPROT: A COMPUTATIONAL WORKBENCH FOR RECOGNITION OF THE STRUCTURAL AND FUNCTIONAL DETERMINANTS IN PROTEIN TERTIARY STRUCTURES 305
A MARKOV MODEL FOR PROTEIN SEQUENCES 317
PROTEOME COMPLEXITY MEASURES BASED ON COUNTING OF DOMAIN-TO-PROTEIN LINKS FOR REPLICATIVE AND NON-REPLICATIVE DOMAINS 329
PART 3. COMPUTATIONAL SYSTEM BIOLOGY 343
A SOFTWARE ARCHITECTURE FOR DEVELOPMENTAL MODELING IN PLANTS: THE COMPUTABLE PLANT PROJECT 345
PREDICTION AND ALIGNMENT OF METABOLIC PATHWAYS 355
GENERAL PRINCIPLES OF ORGANIZATION AND LAWS OF FUNCTIONING IN GOVERNING GENE NETWORKS 367
FROM GRADIENTS TO STRIPES: A LOGICAL ANALYSIS OF DROSOPHILA SEGMENTATION GENETIC NETWORK 379
SELF-OSCILLATIONS IN HYPOTHETICAL GENE NETWORKS 391
PERIODIC TRAJECTORIES AND ANDRONOV-HOPF BIFURCATIONS IN MODELS OF GENE NETWORKS 405
ON THE PROBLEM OF SEARCH FOR STATIONARY POINTS IN REGULATORY CIRCUITS OF GENE NETWORKS 415
MODELING OF GENE EXPRESSION BY THE DELAY EQUATION 421
AGNS--A DATABASE ON EXPRESSION OF ARABIDOPSIS GENES 433
STUDY OF THE INTERACTIONS BETWEEN VIRAL AND HUMAN GENOMES DURING TRANSFORMATION
OF B CELLS WITH EPSTEIN-BARR VIRUS 443
PROBING GENE EXPRESSION: SEQUENCE-SPECIFIC HYBRIDIZATION ON MICROARRAYS 451
DETERMINATION OF THE DEVELOPMENTAL AGE OF A DROSOPHILA EMBRYO FROM CONFOCAL IMAGES
OF ITS SEGMENTATION GENE EXPRESSION PATTERNS 467
PART 4. BIOMOLECULAR DATA AND PROCESSES ANALYSIS 479
TOPICAL CLUSTERING OF BIOMEDICAL ABSTRACTS BY SELF-ORGANIZING MAPS 481
SOFTWARE FOR ANALYSIS OF GENE REGULATORY SEQUENCES BY KNOWLEDGE DISCOVERY METHODS 491
A MATHEMATICAL MODEL OF THE DISCONTINUOUS GENETIC STRUCTURES FIXATION PROCESS 499
REFERENCES 511
INDEX 553
