Volume 13, Number 1, February 1997

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  Kathleen M. Currey, Bruce A. Shapiro: Secondary structure computer prediction of the poliovirus 5' non-coding region is improved by a genetic algorithm. 1-12
• 
  G. Chelvanayagam, Simon Easteal: Correlating patterns in alignments of polymorphic sequences with experimental assays. 13-22
• 
  Asaf A. Salamov, Victor V. Solovyev: Recognition of 3'-processing sites of human mRNA precursors. 23-28
• 
  Q. K. Chen, G. Z. Hertz, Gary D. Stormo: PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices. 29-35
• 
  Eugene V. Korotkov, Maria A. Korotkova, J. S. Tulko: Latent sequence periodicity of some oncogenes and DNA-binding protein genes. 37-44
• 
  J. Alicia Grice, Richard Hughey, Don Speck: Reduced space sequence alignment. 45-53
• 
  Benny Shomer: EMBL sequence submission system--an object-oriented approach to developing interactive data collection systems through the WWW. 55-60
• 
  C. Hoogland, C. Biemont: DROSOPOSON: a knowledge base on chromosomal localization of transposable element insertions in Drosophila. 61-68
• 
  C. Chevalet, Jérôme Gouzy, M. SanCristobal-Gaudy: Regional assignment of genetic markers using a somatic cell hybrid panel: a WWW interactive program available for the pig genome. 69-73
• 
  Kun-Mao Chao, Jinghui Zhang, James Ostell, Webb Miller: A tool for aligning very similar DNA sequences. 75-80
• 
  G. S. Miller, Rainer Fuchs: Post-processing of BLAST results using databases of clustered sequences. 81-87
• 
  Kornelie Frech, Kerstin Quandt, Thomas Werner: Software for the analysis of DNA sequence elements of transcription. 89-97
• 
  Michael G. Roberts, D. A. Phoenix, A. R. Pewsey: An algorithm for the detection of surface-active alpha helices with the potential to anchor proteins at the membrane interface. 99-106
• 
  W. Bains: Hexanucleotide frequency database. 107-108
• 
  Kornelie Frech, P. Dietze, Thomas Werner: ConsInspector 3.0: new library and enhanced functionality. 109-110
• 
  Alexis S. Ivanov, Andrey B. Rumjantsev, Vladlen S. Skvortsov, Alexander I. Archakov: ONIX: an interactive PC program for the examination of protein 3D structure from PDB. 111-113

Volume 13, Number 2, April 1997

• 
  Alexander G. Bachinsky, Andrey A. Yarigin, E. H. Guseva, V. A. Kulichkov, Lily Ph. Nizolenko: A bank of protein family patterns for rapid identification of possible functions of amino acid sequences. 115-122
• 
  J. H. Woods, H. M. Sauro: Elasticities in Metabolic Control Analysis: algebraic derivation of simplified expressions. 123-130
• 
  Eric Rivals, Olivier Delgrange, Jean-Paul Delahaye, Max Dauchet, Marie-Odile Delorme, Alain Hénaut, Emmanuelle Ollivier: Detection of significant patterns by compression algorithms: the case of approximate tandem repeats in DNA sequences. 131-136
• 
  Eric Glémet, Jean-Jacques Codani: LASSAP, a LArge Scale Sequence compArison Package. 137-143
• 
  A. Wozniak: Using video-oriented instructions to speed up sequence comparison. 145-150
• 
  Jacek Blazewicz, Janusz Kaczmarek, Marta Kasprzak, Wojciech T. Markiewicz, Jan Weglarz: Sequential and parallel algorithms for DNA sequencing. 151-158
• 
  R. Varón, F. García Sevilla, M. García-Moreno, F. García-Cánovas, R. Peyro, R. G. Duggleby: Computer program for the equations describing the steady state of enzyme reactions. 159-167
• 
  L. Winder, M. Lefley, B. Smith: A key for freshwater invertebrates using fuzzy logic. 169-174
• 
  Todd Smith, Chris Abajian, Leroy E. Hood: Hopper: software for automating data tracking and flow in DNA sequencing. 175-182
• 
  Y. Tsukamoto, Kyoko Takiguchi, Kenji Satou, Emiko Furuichi, Toshihisa Takagi, Satoru Kuhara: Application of a deductive database system to search for topological and similar three-dimensional structures in protein. 183-190
• 
  Christian Barrett, Richard Hughey, Kevin Karplus: Scoring hidden Markov models. 191-199
• 
  L. Cocea: Search the Human cDNA Database at TIGR. 201-204
• 
  I. Belyi, Pavel A. Pevzner: Software for DNA sequencing by hybridization. 205-210

Volume 13, Number 3, June 1997

• 
  R. R. Mallios: An iterative algorithm for converting a class II MHC binding motif into a quantitative predictive model. 211-215
• 
  Prakash M. Nadkarni: Mapdiff: determining differences between two genomic maps. 217-225
• 
  Yves Van de Peer, Rupert De Wachter: Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. 227-230
• 
  Patrick Aloy, Juan Cedano, Baldomero Oliva, Francesc X. Avilés, Enrique Querol: 'TransMem': a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins. 231-234
• 
  Andrew Rambaut, N. C. Grassly: Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. 235-238
• 
  Rainer Fuchs: Grouper - creation of marker sets for multiplexed genotyping. 239-241
• 
  Anatoly S. Frolov, I. S. Pika, A. M. Eroshkin: ProMSED: protein multiple sequence editor for Windows 3.11/95. 243-248
• 
  Eric Depiereux, G. Baudoux, P. Briffeuil, I. Reginster, Xavier De Bolle, C. Vinals, Ernest Feytmans: Match-Box_server: a multiple sequence alignment tool placing emphasis on reliability. 249-256
• 
  Josef Pánek, Jiri Vohradsky: Object-oriented developmental environment for image-analysis applications: implementation for 2D gel electrophoretogram analysis. 257-262
• 
  S. Tiwari, S. Ramachandran, A. Bhattacharya, S. Bhattacharya, R. Ramaswamy: Prediction of probable genes by Fourier analysis of genomic sequences. 263-270
• 
  L. Ehrlich, C. Munkel, G. Chirico, J. Langowski: A Brownian dynamics model for the chromatin fiber. 271-279
• 
  S. Panzer, L. Cooley, Perry L. Miller: Using explicitly represented biological relationships for database navigation and searching via the World-Wide Web. 281-290
• 
  Gilles Labesse, N. Colloc'h, Joël Pothier, J. P. Mornon: P-SEA: a new efficient assignment of secondary structure from C alpha trace of proteins. 291-295
• 
  András Fiser, Zsuzsanna Dosztányi, István Simon: The role of long-range interactions in defining the secondary structure of proteins is overestimated. 297-301
• 
  Andrew Rambaut, P. H. Harvey, S. Nee: End-Epi: an application for inferring phylogenetic and population dynamical processes from molecular sequences. 303-306
• 
  Julio Rozas, Ricardo Rozas: DnaSP version 2.0: a novel software package for extensive molecular population genetics analysis. 307-311
• 
  Joaquín Dopazo: A new index to find regions showing an unexpected variability or conservation in sequence alignments. 313-317
• 
  Florencio Pazos, O. Olmea, Alfonso Valencia: A graphical interface for correlated mutations and other protein structure prediction methods. 319-321
• 
  Y. Wada, K. Inoue, K. Ohga, H. Yasue: Software tool for gene mapping: gRanch. 323-324

Volume 13, Number 4, August 1997

• 
  William R. Pearson: Identifying distantly related protein sequences. 325-332
• 
  David B. Searls: Linguistic approaches to biological sequences. 333-344
• 
  Burkhard Rost, Seán I. O'Donoghue: Sisyphus and prediction of protein structure. 345-356
• 
  Tatsuya Akutsu, Kentaro Onizuka, Masato Ishikawa: Rapid protein fragment search using hash functions based on the Fourier transform. 357-364
• 
  Steven Salzberg: A method for identifying splice sites and translational start sites in eukaryotic mRNA. 365-376
• 
  J. H. Hofmeyr, A. Cornish-Bowden: The reversible Hill equation: how to incorporate cooperative enzymes into metabolic models. 377-385
• 
  Hiroyuki Toh: Introduction of a distance cut-off into structural alignment by the double dynamic programming algorithm. 387-396
• 
  William Noble Grundy, Timothy L. Bailey, Charles Elkan, Michael E. Baker: Meta-MEME: motif-based hidden Markov models of protein families. 397-406
• 
  P. Durand, L. Canard, J. P. Mornon: Visual BLAST and visual FASTA: graphic workbenches for interactive analysis of full BLAST and FASTA outputs under Microsoft Windows 95/NT. 407-413
• 
  M. Ito, Y. Matsuo, Ken Nishikawa: Prediction of protein secondary structure using the 3D-1D compatibility algorithm. 415-424
• 
  Rob W. W. Hooft, Chris Sander, Gert Vriend: Objectively judging the quality of a protein structure from a Ramachandran plot. 425-430
• 
  V. Biaudet, Franck Samson, Philippe Bessières: Micado - a network-oriented database for microbial genomes. 431-438
• 
  S. Lay, D. Bray: A computer program for the analysis of protein complex formation. 439-444
• 
  J. Schafer, M. Schoniger: DISTREE: a tool for estimating genetic distances between aligned DNA sequences. 445-451
• 
  R. W. Gill, T. Charles Hodgman, C. B. Littler, M. D. Oxer, D. S. Montgomery, S. Taylor, P. Sanseau: A new dynamic tool to perform assembly of expressed sequence tags (ESTs). 453-457
• 
  Bruce A. Shapiro, Jin Chu Wu: Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm. 459-471
• 
  Ross D. King, Mansoor A. S. Saqi, Roger A. Sayle, Michael J. E. Sternberg: DSC: public domain protein secondary structure predication. 473-474
• 
  L. I. Toldo: JaMBW 1.1: Java-based Molecular Biologists' Workbench. 475-476
• 
  Richard Mott: EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA. 477-478
• 
  J. S. Amthor: Calculation of daylength. 479-480
• 
  Miguel A. Andrade, Georg Casari, Antoine de Daruvar, Chris Sander, Reinhard Schneider, Javier Tamames, Alfonso Valencia, Christos A. Ouzounis: Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function. 481-483
• 
  E. Lorenz, S. Leeton, R. J. Owen: A simple method for sizing large fragments of bacterial DNA separated by PFGE. 485-486

Volume 13, Number 5, October 1997

• 
  Ilya N. Shindyalov, Philip E. Bourne: Protein data representation and query using optimized data decomposition. 487-496
• 
  S. Goldberg, P. Ferrand, N. Q. Nguyen, Jean-François Boisvieux, Serge A. Hazout: Bi-dimensional scaling map (BDS-Map): an approach for building large genetic maps. 497-508
• 
  Inge Jonassen: Efficient discovery of conserved patterns using a pattern graph. 509-522
• 
  Carol Soderlund, Ian Longden, Richard Mott: FPC: a system for building contigs from restriction fingerprinted clones. 523-535
• 
  Ronald G. Forsythe Jr., Peter D. Karp, Michael L. Mavrovouniotis: Estimation of equilibrium constants using automated group contribution methods. 537-543
• 
  Benny Shomer: Seqalert - a daily sequence alertness server for the EMBL and SWISSPROT databases. 545-547
• 
  Hugh E. Williams, Justin Zobel: Compression of nucleotide databases for fast searching. 549-554
• 
  Z. Yang: PAML: a program package for phylogenetic analysis by maximum likelihood. 555-556
• 
  W. Gronwald, Robert F. Boyko, Brian D. Sykes: GSC: a graphical program for NMR chemical shift comparison. 557-558
• 
  N. C. Grassly, J. Adachi, Andrew Rambaut: PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees. 559-560
• 
  David S. Wishart, S. Fortin, David R. Woloschuk, W. Wong, T. Rosborough, Gary H. Van Domselaar, Jonathan Schaeffer, Duane Szafron: A platform-independent graphical user interface for SEQSEE and XALIGN. 561-562
• 
  Jean-Paul Rolland, P. Bon, D. Thomas: MACS: automatic counting of objects based on shape recognition. 563-564

Volume 13, Number 6, December 1997

• 
  Ching Zhang, Andrew K. C. Wong: A genetic algorithm for multiple molecular sequence alignment. 565-581
• 
  Jan Gorodkin, Laurie J. Heyer, Søren Brunak, Gary D. Stormo: Displaying the information contents of structural RNA alignments: the structure logos. 583-586
• 
  P. A. Doris, A. Hayward-Lester, J. K. Hays Sr.: Q-RT-PCR: data analysis software for measurement of gene expression by competitive RT-PCR. 587-591
• 
  H. Kato, Y. Takahashi: SS3D-P2: a three dimensional substructure search program for protein motifs based on secondary structure elements. 593-600
• 
  Jérôme Gouzy, P. Eugene, Elizabeth A. Greene, Daniel Kahn, Florence Corpet: XDOM, a graphical tool to analyse domain arrangements in any set of protein sequences. 601-608
• 
  Pascale Guerdoux-Jamet, Dominique Lavenier: SAMBA: hardware accelerator for biological sequence comparison. 609-615
• 
  D. Fenyo: A software tool for the analysis of mass spectrometric disulfide mapping experiments. 617-618
• 
  Hedvig Hegyi, J. M. Lai, Peer Bork: The Sequence Alerting Server - a new WEB server. 619-620
• 
  T. Sicheritz-Ponten: BioWish: a molecular biology command extension to Tcl/Tk. 621-622
• 
  A. S. Law, D. W. Burt: Two applications to facilitate the viewing of database search result files on the Macintosh. 623-624
• 
  Jens Stoye, Vincent Moulton, Andreas W. M. Dress: DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment. 625-626

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