Volume 12, Number 1, February 1996

• 
  Giorgio Grillo, Marcella Attimonelli, Sabino Liuni, Graziano Pesole: CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases. 1-8
• 
  Malcolm F. Wilkins, Lynne Boddy, Colin W. Morris, Richard Jonker: A comparison of some neural and non-neural methods for identification of phytoplankton from flow cytometry data. 9-18
• 
  Sridhar Hannenhalli, W. Feldman, H. F. Lewis, Steven Skiena, Pavel A. Pevzner: Positional sequencing by hybridization. 19-24
• 
  E. S. Carter II, C. S. Tung: NAMOT2 - a redesigned nucleic acid modeling tool: construction of non-canonical DNA structures. 25-30
• 
  Xiaojun Guan, Edward C. Uberbacher: Alignments of DNA and protein sequences containing frameshift errors. 31-40
• 
  Piero Fariselli, Rita Casadio: HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins. 41-48
• 
  Vsevolod Makeev, Vladimir G. Tumanyan: Search of periodicities in primary structure of biopolymers: a general Fourier approach. 49-54
• 
  A. Nandy: Two-dimensional graphical representation of DNA sequences and intron-exon discrimination in intron-rich sequences. 55-62
• 
  Guy Perrière, Jean Thioulouse: On-line tools for sequence retrieval and multivariate statistics in molecular biology. 63-69
• 
  F. Wolfertstetter, Kornelie Frech, Grit Herrmann, Thomas Werner: Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm. 71-80

Volume 12, Number 2, April 1996

• 
  Carlo Caporale, Ciro Sepe, Carla Caruso, Anna M. Garzillo, Vincenzo Buonocore: An algorithm to analyse the hydrolysis pathway of peptides and proteins by sequence analyses of unfractionated digestion mixtures. 81-88
• 
  D. N. Perkins, Terri K. Attwood: XFINGER: a tool for searching and visualising protein fingerprints and patterns. 89-94
• 
  Richard Hughey, Anders Krogh: Hidden Markov models for sequence analysis: extension and analysis of the basic method. 95-107
• 
  Cathy H. Wu, S. Zhao, H.-L. Chen, C. J. Lo, Jerry McLarty: Motif identification neural design for rapid and sensitive protein family search. 109-118
• 
  W. Vahrson, Klaus Hermann, Jürgen Kleffe, Burghardt Wittig: Object-oriented sequence analysis: SCL - a C++ class library. 119-127
• 
  F. Eggenberger, Nicole Redaschi, Reinhard Doelz: FastAlert - an automatic search system to alert about new entries in biological sequence databanks. 129-133
• 
  Jorja G. Henikoff, Steven Henikoff: Using substitution probabilities to improve position-specific scoring matrices. 135-143
• 
  D. Curtis Jamison, Brad Mills, Bruce R. Schatz: An extensible network query unification system for biological databases. 145-150
• 
  G. Schaftenaar, K. Cuelenaere, Jan H. Noordik, Thure Etzold: A Tcl-based SRS v.4 interface. 151-155
• 
  D. S. Prestridge: SIGNAL SCAN 4.0: additional databases and sequence formats. 157-160

Volume 12, Number 3, June 1996

• 
  Igor B. Rogozin, Luciano Milanesi, Nikolay A. Kolchanov: Gene structure prediction using information on homologous protein sequence. 161-170
• 
  Bruce A. Shapiro, Jin Chu Wu: An annealing mutation operator in the genetic algorithms for RNA folding. 171-180
• 
  A. S. Law, D. W. Burt: qValue - a program to calculate comparative measures of genomic reorganisation from cytogenetic and/or linkage information. 181-183
• 
  J. A. Byers: TAXOKEY: a universal taxonomic key program using DOS text files and graphics. 185-189
• 
  Raj K. Singh, D. L. Hoffman, Stephen G. Tell, C. Thomas White: BioSCAN: a network sharable computational resource for searching biosequence databases. 191-196
• 
  Grit Herrmann, A. Schon, R. Brack-Werner, Thomas Werner: CONRAD: a method for identification of variable and conserved regions within proteins by scale-space filtering. 197-203
• 
  A. Nakaya, Kenjiro Taura, K. Yamamoto, Akinori Yonezawa: Visualization of RNA secondary structures using highly parallel computers. 205-211
• 
  Shigehiko Kanaya, Y. Kudo, Yasukazu Nakamura, Toshimichi Ikemura: Detection of genes in Escherichia coli sequences determined by genome projects and prediction of protein production levels, based on multivariate diversity in codon usage. 213-225
• 
  Jürgen Sühnel: Image library of biological macromolecules. 227-229
• 
  Y. Wada, H. Yasue: Development of an animal genome database and its search system. 231-235
• 
  Kirill Degtyarenko, Péter Fábián: The directory of P450-containing systems on WorldWide Web. 237-240
• 
  Jean-Paul Rolland, M. J. Flifla, Mireille Garreau, D. Thomas: IBIS version 3: an OSF/Motif-based interface for IBIS - integrated biological imaging system. 241-245
• 
  O. Matzura, A. Wennborg: RNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows. 247-249
• 
  Ross D. King, C. G. Angus: PM - protein music. 251-252
• 
  V. Proutski, E. Holmes: Primer Master: a new program for the design and analysis of PCR primers. 253-255
• 
  B. I. Osborne: Three sets of Macintosh AppleScripts for the automatic submission of sequence data to the internet BLAST server. 257-258

Volume 12, Number 4, August 1996

• 
  Jin Kim, James R. Cole, Sakti Pramanik: Alignment of possible secondary structures in multiple RNA sequences using simulated annealing. 259-267
• 
  Suchendra M. Bhandarkar, Sridhar Chirravuri, Jonathan Arnold: PARODS - a study of parallel algorithms for ordering DNA sequences. 269-280
• 
  Klaus Lindauer, Cezar Bendic, Jürgen Sühnel: HBexplore - a new tool for identifying and analysing hydrogen bonding patterns in biological macromolecules. 281-289
• 
  Ingrid B. Jakobsen, Simon Easteal: A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. 291-295
• 
  I. Kuznetsov, P. Morozov: GEOMETRY: a software package for nucleotide sequence analysis using statistical geometry in sequence space. 297-301
• 
  William Noble Grundy, Timothy L. Bailey, Charles Elkan: ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool. 303-310
• 
  L. Hu, E. F. Saulinskas, P. Johnson, P. B. Harrington: Development of an expert system for amino acid sequence identification. 311-318
• 
  Cheng Che Chen, Richard O. Chen, Russ B. Altman: Constraining volume by matching the moments of a distance distribution. 319-326
• 
  Kimmen Sjölander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, David Haussler: Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. 327-345
• 
  Joël-Paul Grillasca, Denis Aubert, Richard Planells, N. Domingo, H. Lafont: LITTLE KEVIN: a program for the estimation of protein homology by analysing the amino acid compositions and sequences. 347-351
• 
  M. P. Maradona: Software for microbial fingerprinting by means of the infrared spectra. 353-356
• 
  Roderic D. M. Page: TreeView: an application to display phylogenetic trees on personal computers. 357-358

Volume 12, Number 5, October 1996

• 
  Philipp Bucher, James W. Fickett, Artemis G. Hatzigeorgiou: Computational analysis of transcriptional regulatory elements: a field in flux. 361-362
• 
  C. Fondrat, A. Kalogeropoulos: Approaching the function of new genes by detection of their potential upstream activation sequences in Saccharomyces cerevisiae: application to chromosome III. 363-374
• 
  Craig J. Benham: Computation of DNA structural variability - a new predictor of DNA regulatory regions. 375-381
• 
  Alexander Bolshoy, I. Ioshikhes, Edward N. Trifonov: Applicability of the multiple alignment algorithm for detection of weak patterns: periodically distributed DNA pattern as a study case. 383-389
• 
  G. B. Hutchinson: The prediction of vertebrate promoter regions using differential hexamer frequency analysis. 391-398
• 
  Luciano Milanesi, M. Muselli, P. Arrigo: Hamming-Clustering method for signals prediction in 5' and 3' regions of eukaryotic genes. 399-404
• 
  Kerstin Quandt, Korbinian Grote, Thomas Werner: GenomeInspector: a new approach to detect correlation patterns of elements on genomic sequences. 405-413
• 
  David A. Rosenblueth, Denis Thieffry, Araceli M. Huerta, Heladia Salgado, Julio Collado-Vides: Syntactic recognition of regulatory regions in Escherichia coli. 415-422
• 
  Edward N. Trifonov: Interfering contexts of regulatory sequence elements. 423-429
• 
  Jean-Michel Claverie, Stéphane Audic: The statistical significance of nucleotide position-weight matrix matches. 431-439
• 
  Holger Karas, R. Knüppel, W. Schulz, Heinz Sklenar, Edgar Wingender: Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements. 441-446

Volume 12, Number 6, December 1996

• 
  Jens Hanke, Jens G. Reich: Kohonen map as a visualization tool for the analysis of protein sequences: multiple alignments, domains and segments of secondary structures. 447-454
• 
  F. Hospital, C. Dillmann, A. E. Melchinger: A general algorithm to compute multilocus genotype frequencies under various mating systems. 455-462
• 
  Gilles Labesse: MulBlast 1.0: a multiple alignment of BLAST output to boost protein sequence similarity analysis. 463-467
• 
  Andrew Rambaut, N. C. Grassly, S. Nee, P. H. Harvey: Bi-De: an application for simulating phylogenetic processes. 469-471
• 
  Richard Hughey: Parallel hardware for sequence comparison and alignment. 473-479
• 
  J. Wallman, G. A. Hoelzer, D. J. Melnick: The effects of social structure, geographical structure, and population size on the evolution of mitochondrial DNA: I. A simulation model. 481-489
• 
  U. S. Murty, K. Jamil, D. Krishna, P. J. Reddy: Rule-based system for the fast identification of species of Indian Anopheline mosquitoes. 491-495
• 
  X. Huang, J. Zhang: Methods for comparing a DNA sequence with a protein sequence. 497-506
• 
  Laurent Duret, Elisabeth Gasteiger, Guy Perrière: LALNVIEW: a graphical viewer for pairwise sequence alignments. 507-510
• 
  Ying Xu, Edward C. Uberbacher: A polynomial-time algorithm for a class of protein threading problems. 511-517
• 
  Guy Perrière, J. R. Lobry, Jean Thioulouse: Correspondence discriminant analysis: a multivariate method for comparing classes of protein and nucleic acid sequences. 519-524
• 
  Rob W. W. Hooft, Chris Sander, Michael Scharf, Gert Vriend: The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value. 525-529
• 
  Salvatore Lanzavecchia, L. Tosoni, Pier Luigi Bellon: Fast sinogram computation and the sinogram-based alignment of images. 531-537
• 
  W. J. Heitler: A simple method for the removal of mains interference from pre-recorded electrophysiological data. 539-542
• 
  Nicolas Galtier, Manolo Gouy, Christian Gautier: SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. 543-548
• 
  L. Tosoni, Salvatore Lanzavecchia, Pier Luigi Bellon: Image and volume data rotation with 1- and 3-pass algorithms. 549-552
• 
  J. Lazovic: Selection of amino acid parameters for Fourier transform-based analysis of proteins. 553-562

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