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23 1 12. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J., Basic Local Alignment Search Tool, J. Mol. Biol., 1990, pp.403-410 13. Thompson, J.D., Higgins, D.G., and Gibson, T.J., CLUSTALW: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix, Nucleic Acids Res., 1994,pp. 4673-4680 14. A. Bairoch, Nucleic Acids Res. 24, 1996, pp. 221 15. Kyte, J. and Doolittle, R.F., J. Mol. Biol., 1982, pp. 105 16. Leipe, D. and Soussov, V., http://www3.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html 17. Etzold, T. et al, SRS version 5.1 ftp site ftp://ftp.ebi.ac.uk/pub/software/unix/srs/srs5.1.0.tar.gz 18. Object Management Group (OMG), Common Object Request Broker: Architecture and Specification, Revision 2.0, 1995
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BIOINFORMATICS: Databases and Syste
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BIOINFORMATICS: Databases and Syste
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To Tish, Emily, Miles and Josephine
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TABLE OF CONTENTS INTRODUCTION ....
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INTRODUCTION Stanley Letovsky Bioin
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for wisdom. Where algorithms tend t
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gain performance by distributing qu
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systems described (OPM, BioKleisli,
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DATABASES
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1 NCBI: INTEGRATED DATA FOR MOLECUL
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figure 1, and all flows into the ID
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There are other sets of data that c
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2. Explicit declaration by the hist
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2. W. J. Wilbur, A retrieval system
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2 HOVERGEN: COMPARATIVE ANALYSIS OF
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Figure 1: Phylogenetic tree of the
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fragment. In some cases, a same gen
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Figure 2: Distribution of families
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the user can visualize all the anno
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Selecting orthologous genes with HO
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Thus, HOVERGEN allows one to do exh
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21. Saitou, N. Nei, M. The neighbor
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3 WIT/WIT2: METABOLIC RECONSTRUCTIO
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protein sequence are used (e.g., OR
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After we have accumulated an initia
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Coordinating the Development of Met
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Availability of the Pathways, Softw
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4 ECOCYC: THE RESOURCE AND THE LESS
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epresented as an instance of the cl
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The Gene--Reaction Schematic The ma
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EcoCyc contains extensive informati
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within compound windows uses a conc
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Figure 4: The EcoCyc linear map bro
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Figure 5: The software architecture
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6. Karp. Frame representation and r
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Introduction 5 KEGG: FROM GENES TO
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Binary relations Figure 1 : Level o
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hierarchical text. The genome map i
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(2) Java applets to search, compare
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can be used for gene function assig
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influenzae lacks the upper portion
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Future Directions Figure 4. KEGG as
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Introduction 6 OMIM: ONLINE MENDELI
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The Entry Each OMIM entry is assign
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Searching OMIM is as simple as typi
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How OMIM is Curated OMIM is maintai
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7 GDB: INTEGRATING GENOMIC MAPS Int
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in one of two ways: by being wholly
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Figure 3: Universal Coordinate Disp
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Figure 5: Dispersion of linear (lef
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which minimizes dispersion. The opt
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Figure 10: A piece of an "comprehen
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alignments are better for the speci
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Summary 8 HGMD: THE HUMAN GENE MUTA
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Data coverage and structure 101 By
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Conclusions and Outlook 103 Being b
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Introduction 9 SENSELAB: MODELING H
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107 For the purposes of the rest of
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109 users might advocate creating a
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111 The Associations table describe
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Managing the Object Class Hierarchy
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115 In fig. 2, the Objects and Clas
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117 7. Mirsky JS, Nadkarni PM, Hine
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10 THE MOUSE GENOME DATABASE AND TH
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genetics community fostered the ear
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123 Data acquisition for MGD includ
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125 In February 1998, a ‘cDNA and
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Acknowledgments 127 MGD is funded b
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11 THE EDINBURGH MOUSE ATLAS: BASIC
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expression database under developme
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133 For blastocysts the shape of th
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135 which is a cut at an arbitrary
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137 This defines a viewing directio
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139 plate spline [19] or polynomial
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12 FLYBASE: GENOMIC AND POST- GENOM
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143 Genes, including links via publ
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Public Access to FlyBase Data The c
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147 There are two classes of annota
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149 screens to identify direct or i
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13 MAIZEDB: THE MAIZE GENOME DATABA
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The bins map strategy has been empl
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Clicking on one of the orthologous
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* hyper-text linked to MaizeDB enti
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DISSEMINATION TO EXTERNAL DATABASES
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Appendix 2: part of the Query Form
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Introduction 14 AGIS: USING THE AGR
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Horn Fly--Haematobia Screwworm--Coc
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Figure 2 : Main AGIS Menu 167
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Figure 4 : Available Classes and Su
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Figure 6 : Query by Example and Que
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Figure 8 : Hypertext ACEDB Object a
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15 CGSC: THE E.COLI GENETIC STOCK C
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177 described once for that gene an
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FIGURE 1. A Query for an hsdR- recA
Page 190 and 191: FIGURE 2. A Query for a lacZ-(amber
Page 192 and 193: 183 These are suggestions that dese
Page 194 and 195: SYSTEMS
Page 196 and 197: Introduction 16 OPM: OBJECT-PROTOCO
Page 198 and 199: 189 OPM is a data model whose objec
Page 200 and 201: The OPM Database Development Tools
Page 202 and 203: ased on this query tree. Further qu
Page 204 and 205: 195 Interface, except that one can
Page 206 and 207: 197 Our strategy of providing suppo
Page 208 and 209: Acknowledgments 199 Between 1992 an
Page 210 and 211: Introduction 17 BIOKLEISLI:INTEGRAT
Page 212 and 213: 203 In the remainder of this chapte
Page 214 and 215: pages : “4267-4274", abstract:
Page 216 and 217: BioKleisli in Action: Querying Biom
Page 218 and 219: 209 savings in execution time is si
Page 220 and 221: References 211 13. NCBI ASN. 1 Spec
Page 222 and 223: Introduction 18 SRS: ANALYZING AND
Page 224 and 225: 215 In SRS, databank structures are
Page 226 and 227: 217 Operands also include named set
Page 228 and 229: Figure 1. The SRS Top Page. Figure
Page 230 and 231: Analyzing Data in SRS with Applicat
Page 232 and 233: 223 other databanks, and define spe
Page 234 and 235: Figure 7. A SWISS-PROT entry with i
Page 236 and 237: Figure 8. The results of a query fo
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Page 242 and 243: Introduction 19 BIOLOGY WORKBENCH:
Page 244 and 245: Figure 1. Organization and Flow of
Page 246 and 247: 237 In order to make wrapper develo
Page 248 and 249: the browser window containing a men
Page 250 and 251: either during the current Workbench
Page 252 and 253: PROFILESCAN Comparison of protein o
Page 254 and 255: 20 EBI: CORBA AND THE EBI DATABASES
Page 256 and 257: 247 the Object Request Broker (ORB)
Page 258 and 259: 249 Every database entry is represe
Page 260 and 261: 251 Wrappers with and without State
Page 262 and 263: Discussion 25 3 CORBA and IDL minim
Page 264 and 265: Introduction 21 BIOWIDGETS:REUSABLE
Page 266 and 267: Visualization Solutions 257 Turnkey
Page 268 and 269: 259 The architecture also exploits
Page 270 and 271: possible because the bioWidget arch
Page 272 and 273: 263 4. Gish, Warren (1994-1997). un
Page 274 and 275: 22 ACEDB: THE ACE DATABASE MANAGER
Page 276 and 277: 267 On the other hand, most users c
Page 278 and 279: 269 Street, City and State into "ma
Page 280 and 281: 27 1 to a running database after ed
Page 282 and 283: 273 database the class Map refers t
Page 284 and 285: 275 were waiting for the Biowidget
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Page 288 and 289: Introduction 23 LABBASE: DATA AND W
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28 1 We will use as a running examp
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LabBase Details 283 A LabBase objec
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When the procedure completes, LabFl
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287 sequence-assembly Worker in our
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289 The Worker converts the object
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291 Genome Research and are beginni
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INDEX
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INDEX A of Agricultural Genome Info
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of vertebrate genes, 21-33 developm
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GenBank database query software of,
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Metabolic Pathway Database, 38 Meta
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conversion to ‘gi’ identifiers
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