Table Of Content

I COMPUTER APPLICATIONS Zea IN THE car” (=. BIOSCIENCES Volume 8, 1992 ORL PRESS OXFORD UNIVERSITY PRESS Oxford New York Tokyo ANNUAL AUTHOR INDEX Volume 8 Akrigg,D. 295 Hardison,R.C. 155 Osguthorpe,D.J. 71 Vihinen,M. 35 Alexandrov,N.N. 339 Hazout,S. 255 Ostell,J. 563 Vogt,G. 49 Alvarruiz,A. 549 Heagerty,P. 65 Argos,P. 45,49,599 Henikoff,S. 249 Parry-Smith,D.J. 295,451 Waddington,D. 539 Arnold,J. 467 Heringa,J. 599 Parsons,J.D. 461 Wallace,J.C. 249 Arqués,D.G. 5 Hertz,A.G. 113 Partis,M.D. 1,185 Waterman,M.S. 511 Attwood,T.K. 295,451 Higgins,D.G. 15,137,189, Pasternak,H. 239 Westerhoff,H.V. 443 521,599 Paz,P. 307 Wilkens,L. 23 Babenko, V.E. 79 Hofmann,K. 331 Pearson,W.R. 167,481 Williams,G.W. 149 Badcoe,I.G. 323 Howard,A. 605 Pederson,J.T. 71 Wolf, Y.I. 425 Bercovitz,P.A. 141 Huang,X. 155,511 Pergolizzi,R. 195 Wootton,J.C. 295 Berg,C.M. 227 Perkins,D.N. 295 Bishop,M.J. 149,461 lida, Y. 367 Pevsner,P.A. 129,121 Yoshizawa,C. 23 Bleasby,A.J. 189,295 Innocent,G.T. 97 Piatkowski,U. 587 Blommestijn,G.J.F. 443 Piepenburg,D. 587 Zhang,J. 227 Borodovsky,M. 433 Jamil,K. 209 Pilette,R. 267 Bouffard,G. 563 Jones,D.T. 275 Piqueras,J.R. 307 Brenner,S. 461 Jones,R. 199,377 Ponce,M.R. 603 Brody ,H. 467 Prats,M. 575 Burt,D.W. 539 Kamel,N.N. 311 Byers,J.A. 196 Karp,P.D. 347 Raat,N.J.H. 443 Rapoport,G.N. 113 Karreman,C. 75 CChhaapop,eKl.eMar., J.4E8.1 407 KKeinntcaeird,,MD.. T.5 95 267 RReedaddy,,RP..LJ.. 420079 Chappey,C. 255 Kitamura-Abe,S. 367 Rinke de Wit,T. 595 Chen,J.-H. 243 Kleffe,J. 433 Robson,B. 283 Chevalet,C. 215 Kolchanov,N.A. 529 Rodrigo,M. 549 Clark,S.P. 535 Kozhukhin,C.G. 129 Rodriguez,F. 575 Coatrieux,J.-L. 583 Krishna,D. 209 Rolland,J.-P. 583 CCoocmkicsrkoefty, ,VC..BM.. 7517 9 KKyupdro,,JM. . 293,6470 1 RRouyddt,bKe.rEg., M.2A2.7 ,55673 Consani,I.R. 195 Ruskin,H.J. 579 Cuticchia,A.J. 467 Lawrence,C. 65 Rysavy,F.R. 149 Le,S.-Y. 243 Sagitov,V.R. 79 D’Amaro,J. 595 Lee;C. 227 Schipper,R. 595 Davidow,L.S. 193 Lee,H.P. 23 Schmitz,M. 389 Davison,D. 407 Lee,J. 23,405,555 Schmitz,S. 261 De Bellis,G. 195 Leister,B. 81 Schwartz,S. 155 Depiereux,E. 501 Lépez-Bueno,J.A. 385 Shalev,B.A. 239 Dessaint,F. 409 Lunt,G.G. 71 Sharp,P.M. 521 Dibdin,G.H. 489 Luostarinen,P. 35 Shields,D.C. 521 Dombi,G.W. 475 Liittke,A. 591 Shimbo,M. 367 Dubnick,M. 291,601 Luzzana,M. 195 Shin,D.-G. 227 Shindyalov,I.N. 529 Eberhard,M. 81 Maizel,J.V. 243 Sibbald,P.R. 45 Eernisse,D.J. 177 Makarova,K.S. 425 Soloviev,V.V. 425 Euranto,A. 35 Manoni,M. 195 Sommerfeldt,H. 45,599 Maughan,N.A. 295 Sonnhammer,E.L.L. 443 Ferran,E.A. 39 Mazin,A.V. 425 Spanova,A. 524 Ferrara,P. 39 Michel,C.J. 5 Steger,G. 389 Feytmans,E. 501 Michot,B. 215 Stoehr,P. 137 Fielding,A. 359 Micol,J.L. 603 Stoffel,W. 331 Findlay ,J.B.C. 295 Milanesi,L. 529 Stoffers,H.J. 443 Flifla,M.J. 583 Miller,P.L. 141,167 Stopkotte,C. 81 Friemann,A. 261 Miller,W. 155,481 Streletc,V.B. 529 Fuchs,R. 189,591 Moya,A. 385 Suryanarayana Murty,U. 209 Mrazek,J 29,401,524 Sutherland,R.A. 1 Garavelli,J.S. 407 Garreau,M. 583 Nadkarni,P.M. 141,167 Taylor,W.R. 275 Gefeller,O. 293 Nedelman,J. 65 Thomas,D. 583 Gelfand,M.S. 129 Nevalainen,O. 35 Thornton,J.M. 275 Gibbs,G.P. 149 North,A.C.T. 295 Timberlake,W.E. 467 Greaney ,P.J. 283 Tizado,E.J. 307 Guénoche,A. 569 Orieux,K. 5 Gutierrez,A. 549 Osborne,B.I. 83 Usdin,K. 107 ANNUAL SUBJECT INDEX _ \otmes ADSP Cloning vector protein sequence analysis 451 database system 79 AGE CLUSTAL V analysis of gene evolution 5 multiple sequence alignment, C 189 AIDS incidence CMAP reporting delay distribution, integral equation models 579 contig mapping, VAX/VMS 467 Alignment algorithm CompoundKB protein sequence analysis, DOT matrix 529 intermediary metabolism knowledge base 347 Alignment editor COMPSEQ sequence analysis, MALIGNED 535 large-scale nucleotide sequence analysis 595 AliMac Consensus matrix protein sequence alignment, C 49 Turbo C, multiple alignment 339 Amino acid sequence Contig mapping construction of phylogenetic tree, MacT 591 chromosome reconstruction, CMAP 467 ANAGEL Convex hull DNA fragment length analysis, agarose gel 524 SAS macro, Chull.sas 409 Analysis of context Coordinate estimation subclass method, mRNA precursors 367 restriction map, Genstat 5 539 APL program CSTATUS heat process evaluation, Crank—Nicholson method 549 DNA sequencing software 291 Artificial intelligence Cyanobacteria biological systems, Knowledge Base 113 graphics utility program, MIGS 605 Atari ST sequence analysis, GFA-BASIC 75 Augustinsson plots Database limitations of, enzyme kinetics 475 genomic map data, GeneScape 563 human genome mapping, Unix 149 BASIC sequence searching, PATMAT 249 ecosystem pathways, Macintosh 267 Database management PCR primer design 193 molecular biology 311 word counts in random text, Markov chain 433 Database search BIOSITE sequence pattern matching 377 protein sequence interactive comparison 71 Database searching Blast output natural sequence code 283 parser, Btab 601 Database system Branching process model cloning vector, VECTOR-PC 79 PCR 65 DataMinder Btab molecular biology management tool, Macintosh 107 Blast output parser, sequence database 601 DIROM oligonucleotide directed mutagenesis 425 DNA multiple sequence alignment, CLUSTAL V 189 database search, EMBLSCAN 137 Object-oriented database software, Unix 227 fragment length analysis, agarose gel, ANAGEL 524 oligonucleotide directed mutagenesis, IBM 425 sequence comparison, filtration methods 121 parsing tool, GBPARSE 407 sequence database, GenBank 199 protein sequence alignment, AliMac 49 DNA sequence analysis protein sequence analysis, VAX/VMS 451 Atari ST 75 protein sequence mutation data matrices, MAKEPET 275 hybridization method 569 sequence alignment 481 Markov chain, BASIC 433 sequence analysis, IBM 129 open reading frame 521 sequence analysis, MuSCo 57 DNA — protein interaction sequence analysis, Sun SparcServer 461 linear packing, one-dimensional grid 323 sequence comparison, Sun workstation 511 DNA Aligner C++ phylogenetic analysis, Macintosh 177 object-oriented modelling of cell regulation, IBM 443 DNA sequencing CD-ROM data analysis software 291 DNA database search, EMBLSCAN 137 file exchange 195 cDNA DNA Translator sequence analysis, C 461 phylogenetic analysis, Macintosh 177 Cell regulation DNABIND object-oriented modelling, METASIM 443 nucleotide sequence searching, IBM 401 Chull.sas DOT matrix SAS macro 409 protein sequence analysis, alignment algorithm 529 Subject index Ecology GLOBIC field data analysis software, IBM 587 nucleotide sequence analysis, IBM 29 Ecosystem pathways Graphics utility program carbon transfer, Macintosh 267 MIGS, Quick BASIC 605 Educational software Growth curves PEDIGREE, SEGREGATION, transmission genetics 603 Gompertz function 239 Electron microscopy image-processing software 583 Heat process evaluation EMBLSCAN for spherical foods, APL program 549 DNA database search, CD-ROM 137 Human genome Enzyme kinetics database searching, natural sequence code 283 limitations of Augustinsson plots 475 online service 149 Michae—lM eintsen equation, time correction 575 Hybridization method DNA sequence analysis 569 Hypercard FASTA molecular biology management tool, DataMinder 107 sequence alignment, C 481 HyperPCR Field data analysis PCR optimal annealing temperature 83 software, IBM 587 File exchange IBIS DNA sequencing data 195 integrated biological imaging system, electron micrograph image- Filtration methods processing 583 DNA sequence comparison 121 IBM Finite-difference model DNA fragment length analysis, ANAGEL 524 bacterial film solute diffusion, Quick BASIC 489 epidemiology data analysis 97 FORTRAN field data analysis software 587 PCR analysis 65 nucleotide sequence analysis 129 RNA secondary structure, probability profiles 389 Pascal, analysis of gene evolution 5 sequence analysis, VAX/VMS 535 protein sequence analysis 185 FORTRAN 77 protein sequence interactive comparison 71 DNA database search 137 sequence analysis, Turbo Basic 29 one-dimensional grid, linear packing 323 sequence searching, PATMAT 249 probit analysis 209 spectrum analysis, MULTI 81 protein structure | IDENTITY RNA sequence analysis 15 protein sequence alignment, Turbo BASIC 261 RNAKNOT, pseudoknot prediction 243 Image-processing sequence analysis 57 electron micrograph, IBIS 583 sequence comparison, VAX/VMS 35 Information resource tree edit algorithm, VAX/VMS 215 molecular biology database management 311 VAX/VMS, artificial neural networks 39 Integral equation models VAX/VMS, sequence alignment 501 AIDS incidence, reporting delay distribution 579 Fractal geometry Interactive Matrix Language applications in biology, models, complexity 359 Cox’s proportional hazards regression model 23 Funct G Intermediary metabolism radial distribution function, cluster analysis in cell biology 307 knowledge base, CompoundKB 347 GBPARSE Knowledge base GenBank parsing tool, C 407 artificial intelligence, biological systems 113 GCWIND intermediary metabolism, CompoundKB 347 DNA open reading frame, sequence analysis 521 GenBank Linda flat-file parsing tool 407 genetic linkage analysis, parallel processing 141 sequence database DNA, new entries 199 Linear packing Gene design one-dimensional grid, FORTRAN 77 323 oligonucleotide directed mutagenesis 425 LOAD GeneScape DNA sequencing software 291 relational database, genomic map data, Macintosh 563 Genetic linkage Macintosh parallel processing, Unix workstations 141 molecular biology management tool, DataMinder 107 Genome phylogenetic analysis, Hypercard 177 Object-oriented database software 227 relational database, GeneScape 563 Genstat 5 Macintosh Hypercard restriction map coordinate estimation, microVAX 539 PCR, HyperPCR 83 GEOSEQ MacT sequence alignment, statistical geometry 385 construction of phylogenetic tree, Quick BASIC 591 GFA-BASIC MAKEPET sequence analysis, Atari ST 75 mutation data matrices, C 275 a 616 Subject index MALIGNED Parallel processing multiple alignment editor, sequence analysis 535 genetic linkage analysis, Linda 141 Markov chain protein sequence alignment, AliMac 49 DNA, word counts in random text 433 Parsing tool MATCH-BOX GenBank flat-file 407 protein sequence alignment, FORTRAN 77 501 Pascal METASIM analysis of gene evolution 5 object-oriented modelling of cell regulation 443 nucleotide sequence search 45 Michaelis— Menten equation Statistical geometry, sequence alignment 385 limitations of Augustinsson plots 475 PATMAT time correction for enzyme kinetics 575 sequence searching, IBM 249 MicroVAX Pattern matching FORTRAN 77, protein structure | sequence database search, parallel computer 377 MIGS PCR miscellaneous image generation system, graphics utility program, analysis with internal controls, branching process model 65 Quick BASIC 605 optimal annealing temperature, Macintosh Hypercard 83 MISMATCH primer design, MISMATCH 193 PCR primer design, BASIC 193 PEDIGREE Models educational software, transmission genetics 603 fractal geometry, applications in biology 359 Phylogenetic analysis Molecular biology sequence analysis, Macintosh 177 database management, information resource 311 Phylogenetic tree DataMinder, Hypercard 107 amino acid sequence, MacT 591 Molecular evolution Probability profiles analysis of gene evolution 5 RNA secondary structure, FORTRAN 389 MOMENT Probit analysis protein sequence analysis, IBM 185 mosquito control, FORTRAN 77 209 mRNA precursors PROFILEGRAPH analysis of context of splice site signals, mRNA precursors 367 protein sequence analysis, graphical tool 331 MULTI Protein spectrum analysis 81 clustering, artificial neural networks 39 MULTICOMP Protein sequence sequence comparison, FORTRAN 77 35 alignment, IDENTITY 261 Multiple alignment alignment, MATCH-BOX 501 consensus matrix 339 alignment, parallel processing, AliMac 49 MuSCo hydrophobic moments, MOMENT 185 sequence analysis, common patterns 57 interactive comparison, BIOSITE 71 mutation data matrices, MAKEPET 275 Protein sequence analysis Natural sequence code ADSP 451 human genome database searching 283 alignment algorithm 529 Neural networks Atari ST 75 artificial, protein clustering 39 graphical tool 331 Neuroblastoma region delineation 255 epidemiology data analysis 97 SERPENT 295 Nucleic acids similarity level, structural resolution 599 gene design, DIROM 425 Protein structure Nucleotide antibody binding site 1 large-scale sequence analysis, COMPSEQ 595 Object-oriented database Quick BASIC Escherichia coli genome 227 cluster analysis, Funct G 307 Object-oriented modelling IBM, finite-difference model 489 cell regulation, METASIM 443 reference citation search 196 OBSTRUCT protein sequence analysis, similarity level, structural resolution 599 Open reading frame Radial distribution function sequence analysis, GCWIND 521 cluster analysis in cell biology 307 Ordinal response data Rdb cumulative logit model, SAS program 555 contig mapping, VAX/VMS 467 Overseer REF-LIST nucleotide sequence search 45 reference citation search, Quick BASIC 196 Regression model Parallel computation Cox’s proportional hazards, survival curves 23 machine independent, sequence comparison 167 Restriction map Parallel computer fragment length, coordinate estimation, Genstat 5 539 sequence pattern matching, database search 377 sequence comparison, C 511 Subject index a RNA Subclass method pseudoknot prediction, RNAKNOT 243 mRNA precursors, analysis of context of splice site signals 367 secondary structure, probability profiles 389 Survival curves sequence analysis, FORTRAN 77 15 Cox’s proportional hazards regression model, Interactive Matrix tree edit algorithm, secondary structure 215 Language 23 RNAKNOT RNA pseudoknot prediction, FORTRAN 77 243 Transmission genetics educational software, PEDIGREE, SEGREGATION 603 SAS macro Tree edit algorithm Chull.sas, convex hull of sets of points 409 RNA secondary structure, FORTRAN 77 215 SAS program Turbo BASIC cumulative logit model for ordinal response data 555 nucleotide sequence searching, DNABIND 401 SEGREGATION protein sequence alignment, MS-DOS 261 educational software, transmission genetics 603 sequence analysis 29 SEQSTAT Turbo C DNA sequencing software 291 protein sequence interactive comparison 71 Sequence multiple alignment, consensus matrix 339 pattern matching, parallel computer database search 377 Turbo Pascal Sequence alignment DNA sequence analysis 521 CLUSTAL V, C 189 graphical tool, PROFILEGRAPH 331 FASTA, C 481 protein sequence analysis 185 IDENTITY, Turbo BASIC 261 Turbo Prolog MATCH-BOX, FORTRAN 77 501 cloning vector database system 79 Statistical geometry, GEOSEQ 385 Sequence analysis Unix ADSP, C 451 human genome mapping, online service 149 alignment algorithm, DOT matrix 529 image-processing software 583 cDNA, ICAtool 461 Object-oriented database software, C 227 common patterns, MuSCo 57 parallel processing, genetic linkage analysis, Linda 141 DNA, hybridization method 569 sequence analysis, SIM 155 dotplot 75 GLOBIC 29 Variance comparison local similarity, parallelization, SIM 155 between correlated samples 405 Markov models, IBM 129 VAX/VMS multiple alignment editor, MALIGNED 535 artificial neural networks, FORTRAN 77 39 nucleotide, COMPSEQ 595 chromosome reconstruction, CMAP 467 ordination 15 nucleotide sequence search 45 phylogenetic analysis, Macintosh 177 RNA sequence analysis, FORTRAN 77 15 protein, OBSTRUCT 599 sequence comparison, FORTRAN 77 35 protein, region delineation 255 tree edit algorithm, FORTRAN 77 215 protein, SERPENT 295 VECTOR-PC Sequence comparison cloning vector database system 79 filtration methods, statistical distance 121 machine independent parallel computation, C-Linda 167 MULTICOMP 35 restriction map, C 511 Sequence database Btab, Blast output parser 601 new entries, GenBank 199 Sequence search Overseer 45 nucleotide, DNABIND 401 SERPENT protein sequence analysis, information storage 295 SIM sequence analysis, local similarity 155 Solute diffusion bacterial film, finite-difference model 489 Spectrophotometry MULTI, spectrum analysis 81 Statistical analysis cumulative logit model for ordinal response data 555 variance comparison between correlated samples 405 Statistical packages measures of association, delta method 293 STATUS DNA sequencing software 291 A 618