Table Of ContentBIOINFORMATICS OF GENOME
REGULATION AND STRUCTURE
BIOINFORMATICS OF GENOME
REGULATION AND STRUCTURE
Edited by
NIKOLAY KOLCHANOV
Institute of Cytology & Genetics, Siberian Branch
of the Russian Academy of Sciences, Novosibirsk, Russia
RALF HOFESTAEDT
Bielefeld University, Bielefeld, Germany
....
Springer Science+ Business Media, LLC
''
Library of Congress Cataloging-in-Publication Data
A C.I.P. Catalogue record for this book is available
from the Library of Congress.
Title: Bioinformatics of Genome Regulation and Structure
Editor: Ralf Hofestaedt and Nikolay Kolchanov
ISBN 978-1-4757-4613-6 ISBN 978-1-4419-7152-4 (eBook)
DOI 10.1007/978-1-4419-7152-4
Copyright © 2004 by Springer Science+Business Media New York
Originally published by Kluwer Academic Publishers in 2004
All rights reserved. No part of this work may be reproduced, stored in a retrieval
system, or transmitted in any form or by any means, electronic, mechanical,
photocopying, microfilming, recording, or otherwise, without the written permission
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Permission for books published in Europe:
Contents
Contributing Authors XI
Preface XIII
Foreword XV
PART 1. COMPUTATIONAL GENOMICS 1
NUCLEOSOMAL DNA ORGANIZATION: AN INTEGRATED
INFORMATION SYSTEM
V.G. Levitsky, A. V. Katokhin, O.A. Podkolodnaya, D.P. Furman.............. .... . 3
USING CHANGE IN LOCAL DNA SEQUENCE COMPLEXITY
AS A POINTER TO THE MECHANISM OF MUTAGENESIS
IN INHERITED DISEASE
N.A. Chuzhanova, D.N. Cooper....................... ... ......... .................. .... ...... .. .... 13
PROPERTIES OF INSERTION REGIONS OF DROSOPHilA LTR
RETROTRANSPOSONS
D.P. Furman, D. Yu. Oshchepkov, M.A. Pozdnyakov, A. V. Katokhin .... ........ 21
COMPOSITIONAL ASYMMETRIES AND PREDICTED
ORIGINS OF REPLICATION OF THE SACCHAROMYCES
CEREVISIAE GENOME
J.O. Korbel, H.E. Assmus, S.M. Kielbasa, H. Herzel.................................... 33
REVEALING AND FUNCTIONAL ANALYSIS OF tRNA-LIKE
SEQUENCES IN VARIOUS GENOMES
F.E. Frenkel, M.B. Chaley, E. V. Korotkov, K.G. Skryabin............................ 39
TYPE-SPECIFIC FEATURES OF THE STRUCTURE
OF THE tRNA GENE PROMOTERS
Yu. V. Kondrakhin, I. B. Rogozin, T.M. Naykova, N.S. Yudin,
M.l. Voevoda, A.G. Romashchenko................ .. ........ ...................... ............... 47
MATHEMATICAL TOOLS FOR REGULATORY
SIGNALS EXTRACTION
M. Regnier.... ....... .......................................................................................... 61
ARGO_V IEWER: A PACKAGE FOR RECOGNITION
AND ANALYSIS OF REGULATORY ELEMENTS
IN EUKARYOTIC GENES
0 . V. Vishnevsky, E. A. Ananko, E. V. lgnatieva, O.A. Podkolodnaya,
l.L. Stepanenko ......................................... .. .................. ................ ...... ........... 71
TRANSCRIPTION REGULATORY REGIONS DATABASE
(TRRD): DESCRIPTION OF TRANSCRIPTION REGULATION
AND THE MAIN CAPABILITIES OF THE DATABASE
E. V. /gnatieva, E.A. Ananko, O.A. Podkolodnaya,
l.L. Stepanenko, T.M. Khlebodarova, T.l. Merkulova,
M.A. Pozdnyakov, A.L. Proscura, D.A. Grigorovich,
N.L. Podkolodny, A.N. Naumochkin, A. G. Romashchenko,
N.A. Kolchanov............................................................ .............................. .... 81
SITECON-A TOOL FOR ANALYSIS OF DNA
PHYSICOCHEMICAL AND CONFORMATIONAL PROPERTIES:
E2F/DP TRANSCRIPTION FACTOR BINDING SITE ANALYSIS
AND RECOGNITION
D. Yu. Oshchepkov, I. I. Turnaev, M.A. Pozdnyakov, L. Milanesi,
E. E. Vityaev, N.A. Kolchanov ..... .... .............................. ................................. 93
LOCAL SECONDARY STRUCTURE MAY BE A CRITICAL
CHARACTERISTIC INFLUENCING TRANSLATION
OF UNICELLULAR ORGANISMS mRNA
Yu.G. Matushkin, V.A. Likhoshvai, A. V. Kochetov...................................... 103
COMPUTER ANALYSIS OF miRNA-mRNA DUPLEXES
AND ITS APPLICATION TO PREDICTING POSSIBLE TARGET
mRNAS OF ARAB/DOPSIS
N.A. Omelyanchuk, D.G. Vorobiev.............................................................. 115
VI
CORRELATIONS BETWEEN SEQUENCE FEATURES
OF YEAST GENES FUNCTIONAL REGIONS AND THE LEVEL
OF EXPRESSION
A. G. Pichueva, A.V . Kochetov, L. Milanesi, Yu. V. Kondrakhin,
N.A. Kolchanov.. ....... ... ... ............. ...... .... ....... ... ..... ... .............. ..... ...... ....... .... 125
PART2. COMPUTATIONAL STRUCTURAL BIOLOGY 133
LATENT PERIODICITY OF MANY DOMAINS IN PROTEIN
SEQUENCES REFLECTS THEIR STRUCTURE, FUNCTION,
AND EVOLUTION
A.A. Laskin, E. V. Korotkov, N.A. Kudryashov... .... .......... ................ .... ........ 135
LOGICAL ANALYSIS OF DATA AS A PREDICTOR
OF PROTEIN SECONDARY STRUCTURES
J. Blaiewicz, P.L. Hammer, P. Lukasiak. ... ..... .... ............. ....... .... ...... .......... 145
STRUCTURE-SPECIFICITY RELATIONSHIP
IN PROTEIN-DNA RECOGNITION
H. Kono, A. Sarai .. ............. ...... .... ........ .... ........... ....... ......... ....... ....... .......... 155
MACROMOLECULAR MODELING AS A TOOL
FOR EXPANDING BIOINFORMAT ICS DATABASES
Yu.N. Vorobjev...... ... ..... .............. ...................... .. ...... ... ........... ........... ..... .... . 163
GRAPHIC REPRESENTATION OF EQUILIBRIUM
AND KINETICS IN OLIGOPEPTIDES: TIME-DEPENDENT
FREE ENERGY DISCONNECTIVITY GRAPHS
A. V. Gavrilov, S.F. Chekmarev...... ..... ... .. ..... ... .. .. .. ... .... ... .. .......... ...... ... ..... .. 171
SOLV ENT ELECTROSTATIC SCREENING
IN PROTEIN SIMULATIONS
S.M. Schwarz[, S. Fischer, J.C. Smith. ....... ......... .... .... .. ... ..... ....................... 179
PDBSITESCAN: A PROGRAM SEARCHING
FOR FUNCTIONAL SITES IN PROTEIN 3D STRUCTURES
V.A. lvanisenko, S.S. Pintus, D.A. Grigorovich, L.N. lvanisenko,
V.A. Debelov, AM. . Matsokin ............... ........ ... ...... ........ ......................... ..... 185
A GENETIC ALGORITHM
FOR THE INVERSE FOLDING OF RNA
I. I. Titov, A. Yu. Palyanov......... ............... ..... .. ........ ... .... .. ..... .. .. ..... .. ........ ... .. 193
VII
SIGNAL TRANSDUCTION PATHWAYS INITIATED VIA CELL
SURFACE RECEPTOR CD150: IN SILICO AND IN VITRO
ANALYSIS
S.P. Sidorenko, S. V. Mikhalap, L.M. Shlapatska, M.Y . Yurchenko,
Y.M. Akimov, V.F. Chekhun... ..... .. ... ....... ............... .... ..... ... ... ..... ... .... .... ... .... 203
PART3. COMPUTATIONAL EVOLUTIONARY BIOLOGY 211
STUDY OF THE SPECIFIC CONTEXTUAL FEATURES
OF TRANSLATION INITIATION AND TERMINATION SITES
IN SACCHAROMYCES CEREVISIAE
0 . V. Vishnevsky, I. V. Avdeeva, A. V. Kochetov .............. .... .... ... ..... ..... ...... ... 213
CONTRIBUTION OF COORDINATED SUBSTITUTIONS
TO THE CONSTANCY OF PHYSICOCHEMICAL PROPERTIES
OF ATP-BINDING LOOP IN PROTEIN KINASES
D.A. Afonnikov.. ... .. .............. .... .. .. . .. .. .. ..... .... ... .. ..... .. .. ... .. .. .. .. .. .. .. .. .. ... .. .. .. .. .. 223
SPORADIC EMERGENCE OF LATENT PHENOTYPE
DURING EVOLUTION
V.A. Likhoshvai, Yu.G. Matushkin .......... .. ..... ....... ..... .... ..... ........ ......... ........ 231
SIMILARITY ANALYSIS OF INVERSION BANDING
SEQUENCES IN CHROMOSOMES OF CHIRONOMUS SPECIES
(BREAKPOINT PHYLOGENY)
l.l. Kiknadze, L.l. Gunderina, A.G. !stamina, V.D. Gusev,
L.A. Nemytikova..... ........ ... ... ....... .. ...... ................. .. ... ..... ... ......... .... ........... .. . 245
PART4. SYSTEM COMPUTATIONAL BIOLOGY 255
INTEGRATIVE ANALYSIS OF GENE NETWORKS USING
DYNAMIC PROCESS PATTERN MODELLING
A. Freier, M. Lange, R. Hofestaedt... ... .. ...... ... .... ..... .... .. .... ...... .. ..... ... ..... ..... 257
DEVELOPMENT AND ANALYSIS OF MODELS OF GENETIC
AND METABOLIC NETWORKS AND SIGNAL
TRANSDUCTION PATHWAYS IN THE GENENET SYSTEM
E.A. Ananko, K.A. Loktev, N.L. Podkolodny... .... ....... .... ... ..... ... ...... ... ..... ..... 265
EXTENSION OF CELL CYCLE GENE NETWORK
DESCRIPTION BASED ON PREDICTION OF POTENTIAL
BINDING SITES FOR E2F TRANSCRIPTION FACTOR
I. I. Turnaev, D. Yu. Oshchepkov, O.A. Podkolodnaya .... ..... .... ............. ....... 273
VIII
MATHEMATICAL SIMULATION OF DYNAMICS
OF MACROPHAGE GENE NETWORK ACTIVATED
BY LIPOPOLY SACCHARIDES AND/OR INTERFERON-g
E.A. Nedosekina, E.A. Ananko, L. Milanesi, V.A. Likhoshvai,
N.A . Kolchanov. .... .. ... .... .... .... .......... .. .... .... ..... ... ....... ..... ......... ... ......... ....... .. 283
COMPUTER DYNAMIC MODELING OF THE GENE NETWORK
CONTROLLING INTRACELLULAR CHOLESTEROL
HOMEOSTASIS
A. V. Ratushny, E. V. lgnatieva, V.A. Likhoshvai ... ... . .. .. ..... .. ... ... . .. . .... .. .... .. .. 293
AN INVESTIGATION OF THE STRUCTURAL STABILITY
OF DROSOPHilA CONTROL GENE SUBNETWORK
IN COMPUTER EXPERIMENTS
A. V. Galimzyanov, R.N. Tchuraev ... ..... ......... ........ ....... ...... .. .... ........ ..... .... .. 301
MODELING PLANT DEVELOPMENT WITH GENE
REGULATION NETWORKS INCLUDING SIGNALING
AND CELL DIVISION
H. Jonsson, B.E. Shapiro, E.M. Meyerowitz, E. Mjolsness. .. .... .. ..... .... .... .. .. 311
THE GLOBAL OPERATION MODES
OF GENE NETWORKS DETERMINED BY THE STRUCTURE
OF NEGATIVE FEEDBACKS
V.A. Likhoshvai, S.l. Fadeev, Yu.G. Matushkin. ....... .. ..... .. .......... ........ ... ..... 319
STATISTICAL ANALYSIS OF MICROARRAY DATA:
IDENTIFICATION AND CLASSIFICATION
OF YEAST CELL CYCLE GENES
Yu. V. Kondrakhin, O.A. Podkolodnaya, A. V. Kochetov, G.N. Erokhin,
N.A. Kolchanov.. ... .... ..... .... ..... ... ........ ........... .... .. ....... ......... ..... .... ......... .... ... 331
References 343
Index 371
IX
Contributing Authors
D.A. Afonnikov E.V. Ignatieva
Y.M. Akimov A.G. Istomina
E.A. Ananko V.A. Ivanisenko
H.E. Assmus L.N. Ivanisenko
LV. Avdeeva H. Jonsson
J. Blazewicz A. V. Katokhin
M.B. Chaley T.M. Khlebodarova
V.F. Chekhun S.M. Kielbasa
S.F. Chekmarev I.I. Kiknadze
N.A. Chuzhanova A. V. Kochetov
D.N. Cooper N.A. Kolchanov
V .A. Debelov Yu. V. Kondrakhin
G.N. Erokhin H. Kono
S.I. Fadeev J.O. Korbel
S. Fischer E.V. Korotkov
A. Freier N.A. Kudryashov
F.E. Frenkel M. Lange
D.P. Furman A.A. Laskin
A. V. Galimzyanov V.G. Levitsky
A.V. Gavrilov V .A. Likhoshvai
D.A. Grigorovich K.A. Loktev
L.I. Gunderina P. Lukasiak
V.D. Gusev A.M. Matsokin
P.L. Hammer Yu.G. Matushkin
H. Herzel T.I. Merkulova
R. Hofestaedt E.M. Meyerowitz
