Computer Applications in the Biosciences, Volume 12

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
  

Last update Fri May 24 20:02:15 2013 CET by the DBLP Team — Data released under the ODC-BY 1.0 license — See also our legal information page