Genome exploitation : data mining the genome /

Table Of Contents:

Rice Genome Sequencing and Data Mining Resources 1(12)

Baltazar A. Antonio

Yoshiaki Nagamura

Nobukasu Namiki

Takashi Matsumoto

Takuji Sasaki

Introduction 1(1)

Rice Genome Sequencing 2(2)

Rice Genome Informatics 4(2)

Functional Genomics Resources 6(2)

Towards an Integrated Data Mining Resource 8(1)

References 9(4)

Application of Evolutionary Computation to Bioinformatics 13(18)

Daniel Ashlock

Introduction 13(1)

Evolutionary Computation 14(2)

Finding a Transposon Insertion Motif 16(2)

PCR Primer Picking 18(6)

DNA Bar Code Location 24(4)

Summary 28(1)

References 29(2)

Architectures for Integration of Data and Applications: Lessons from Integration Projects 31(18)

William D. Beavis

Introduction 31(4)

A Web-Accessible Data Warehouse (TAIR) 35(2)

Description 35(2)

Lessons 37(1)

An Automated Analysis and Annotation Pipeline (XGI) 37(3)

Description 37(2)

Lessons 39(1)

An Open Source Integrated System (Genex-Lite) 40(3)

Introduction 40(3)

Lessons 43(1)

Loose Coupling Integration (ISYS) 43(2)

Description 43(2)

Lessons 45(1)

Summary of Lessons Learned from All Integration Projects 45(1)

References 46(3)

Functional Genomics Approach to Elucidate the Regulation of Vascular Development in Poplar 49(14)

Rishikesh P. Bhalerao

Goran Sandberg

Introduction 49(2)

Poplar as a Model for Studying Formation 51(1)

Elucidating the Control of Secondary Xylem Development 51(5)

The Role of Aux/IAA Genes in Regulation of Secondary Xylem Development 51(2)

Genomics Approach to Elucidation of Secondary Xylem Development 53(3)

The Seasonal Control of Cambial Activity 56(3)

Large Scale Sequencing of Active and Dormant Cambial Libraries 57(1)

Transcript Profiling of Active and Dormant Cambium 58(1)

Future Perspectives 59(1)

Arabidopsis as Test Bed for Rapidly Identifying Genes Involved in Vascular Development 59(1)

Rapid Analysis of Gene Function of Poplar Genes with Unknown Function 60(1)

Conclusions 60(1)

References 61(2)

Novel Tools for Plant Genome Annotation and Applications to Arabidopsis and Rice 63(14)

Volker Brendel

Introduction 63(1)

Boon and Bane of the Industrialization of Molecular Biology and Genetics 64(1)

The Gene Structure Annotation Problem 65(1)

Gene Structure Annotation by Spliced Alignment 65(3)

The Case for a Community Approach to Annotation 68(7)

Perspective 75(1)

References 75(2)

FCModeler: Dynamic Graph Display and Fuzzy Modeling of Metabolic Maps 77(12)

Julie A. Dickerson

Modeling Metabolic Networks 77(1)

Metabolic Networking Database 78(1)

Modeling Metabolic Relationships 79(3)

Graphing the Metabolic Map: FCModeler 80(1)

Modeling Metabolic Networks Using Fuzzy Cognitive Maps 81(1)

Cycle Analysis in Metabolic Networks 82(1)

Representing Metabolic Pathways in Virtual Reality 82(3)

3-D Network Visualization 83(1)

User Interaction and Navigation 83(2)

Virtual Cell Representation 85(1)

Summary 85(1)

References 86(3)

Old Methods for New Ideas: Genetic Dissection of the Determinants of Gene Expression Levels 89(20)

Kyunga Kim

Marilyn A.L. West

Richard W. Michelmore

Dina A. St. Clair

R.W. Doerge

Introduction 89(1)

Genetical Genomics 90(1)

Methods 91(6)

Dye Swap Experimental Design 92(1)

Modelling Determinants of Expression Level Polymorphisms 92(2)

Experimental Design for Expression Level Polymorphism Analysis 94(2)

Implementation of ELP Mapping Using Existing Multiple Trait Mapping Methodology 96(1)

Simulation Study 97(7)

Simulation of RIL Genotypes 97(1)

Simulation of Gene Expression Simulation 98(1)

Multiple Gene/trait JZmapqtl Mapping 99(2)

Simulation Results 101(3)

Discussion 104(1)

References 105(4)

Charting Contig--Component Relationships within the Triticeae: Exploiting the Genome 109(12)

Gerard R. Lazo

Nancy Lui

Frank M. You

David D. Hummel

Shiaoman Chao

Olin D. Anderson

Introduction 109(1)

Approach 110(7)

Display Settings 111(1)

Discerning Contig-Component Relationships 112(3)

Other Applications 115(2)

Software 117(1)

Discussion 117(2)

References 119(2)

Protein Family Classification with Discriminant Function Analysis 121(12)

Etsuko N. Moriyama

Junhyong Kim

Introduction 121(5)

Protein Classification Methods 122(1)

Pros and Cons for the Current Protein Classification Tools 122(2)

G-protein Coupled Receptor Super Family 124(2)

Discriminant Analysis 126(4)

Input Variables 126(1)

Datasets 127(1)

Discrimination Methods 127(1)

Performance Comparisons for the GPCR Protein Family Classification 128(2)

Development of a Hierarchical Classification Algorithm 130(1)

References 131(2)

Exploiting Natural Variation to Understand Gene Function in Pine 133(12)

David B. Neale

Garth R. Brown

Introduction 133(1)

Association Mapping in Plants 134(1)

Pine is a Model Species to Understand Allelic Effects on Phenotypes 134(4)

Pines are Evolutionarily Much Older than Crop Species 135(1)

Pines are Mostly Undomesticated and Are Found in Large Random-Mating Populations 135(1)

Clonal Replication Permits Precise Evaluation of Phenotypes 136(1)

Direct Determination of Haplotype 136(2)

Association Mapping in Loblolly Pine 138(5)

Clonal Association Mapping Populations and Phenotypic Evaluations 138(1)

SNP Discovery, Nucleotide Diversity and Linkage Disequilibrium 138(4)

Associations between SNP Genotype and Phenotype 142(1)

Summary 143(1)

References 143(2)

Merging Analyses of Predisposition and Physiology Towards Polygene Discovery 145(18)

Daniel Pomp

Mark F. Allan

Stephanie R. Wesolowsk

Introduction 145(2)

Significance 147(1)

Background 147(2)

Transcriptome Mapping: A New Experimental Paradigm for Analysis of Complex Trait Genetics 149(5)

Expected Outcomes from the Transcriptome Mapping Paradigm 151(3)

Future Directions for Transcriptome Mapping 154(1)

Statistical Issues 154(1)

Implementation 155(3)

References 158(5)

Mining the EST Databases to Determine Evolutionary Events in the Legumes and Grasses 163(20)

Jessica A. Schlueter

Phillip Dixon

Cheryl Granger

Randy C. Shoemaker

Introduction 163(1)

Evolutionary History of Legumes and Grasses 164(2)

Identification of Duplicated Contigs 166(1)

Pairwise Distance Measures and Mixtures of Normal Distributions 167(2)

Coalesence Estimates 169(6)

Positively Selected Genes 175(2)

Summary 177(1)

References 178(5)

A Biologist's View of Systems Integration Systems Biology: The Pathogen Portal Project 183(14)

R. Lathigra

Y. He

R.R. Vines

E.K. Nordberg

B.W.S. Sobral

Introduction 183(2)

Illustration of PathPort 185(6)

Use of PathPort for Genome Annotation and Comparison 185(2)

PathPort as a Pathogen Information Resource 187(4)

Other PathPort Tools for Functional Annotation 191(1)

Discussion 192(3)

References 195(2)

Alignment of Wheat and Rice Structural Genomics Resources 197(14)

Daryl J. Somers

Sylvie Cloutier

Travis Banks

Introduction 197(1)

Primary Structural Genomics Resources 198(4)

Genetic Maps 198(1)

QTL Mapping 199(1)

EST Sequences 199(1)

Chinese Spring Deletion Lines 199(1)

Large Insert Libraries 200(1)

Rice Genome Sequence 201(1)

SNPs in Wheat ESTs 202(2)

Nested PCR Analysis of SNPs 202(1)

Development of Genome-Specific SNPs 203(1)

Wheat/Rice Virtual Mapping (WRVM) 204(3)

Implementation of `WRVM' 207(1)

Summary 207(2)

References 209(2)

Computational Identification of Legume-Specific Genes 211(36)

Michelle A. Graham

Kevin A. T. Silverstein

Steven B. Cannon

Kathryn A. VandenBosch

Identification of Sequences of Interest from Public Databases 211(1)

Importance of Legumes 212(1)

Databases of Expressed Sequence Tags 212(2)

Data Mining the TIGR Gene Indices 213(1)

Data Mining the M. truncatula MtDB Database 213(1)

Identification of Legume-Specific Genes 214(4)

Using BLAST to Identify Legume-Specific Genes 214(3)

Are the Identified Legume-Specific TCs Really Legume-Specific? 217(1)

How Can a Gene's Function be Determined When BLAST Fails to Find a Homolog? 218(5)

Single Linkage Clustering 218(2)

Motif Searching 220(3)

Future Goals 223(1)

References 223(6)

ABSTRACTS

Brahms and Beergenes: Information Management for Genetic Research on Barley and Oat 229(2)

Jean Gerster

Nicholas A. Tinker

Yella Jovich-Zahirovich

Anissa Lybaert

Shaolin Liu

Stephen J. Molnar

Diane E. Mather

Microcolinearity in the Allotetraploid Gossypium hirsutum 231(2)

C. Grover

H. Kim

R.A. Wing

J.F. Wendel

Determining the Chromosomal Location of the Wheat Leaf Rust Resistance Gene LrW1 233(2)

C. Hiebert

J. Thomas

B. McCallum

Characterization of EST Libraries from Drought-Stressed Leaves and Penetrated Roots of Rice 235(2)

Md S. Pathan

William G. Spollen

Mark Fredricksen

Hans J. Bohnert

Deshui Zhang

Henry T. Nguyen

The Phylogenetic Utility of N-Length DNA Strings in Plants 237(2)

Ryan Rapp

J. Gordon Burleigh

Telocentrics as a Breeding Tool in Wheat 239(2)

Erica Riedel

Julian Thomas

Comparative DNA Sequence Analysis of Wheat and Rice Genomes 241(2)

Mark E. Sorrells

Mauricio La Rota

Marker Assisted Backcrossing---Some Lessons from Simulation 243(2)

Julian Thomas

Daryl Somers

Ceregenedb: A Database of Coding Sequence Conservation Between Rice and Nonrice Cereals and Arabidopsis 245(2)

Shibo Zhang

Brian C. Thomas

Peggy G. Lemaux
Index 247