Computer Applications in the Biosciences, Volume 4

Volume 4, Number 1, March 1988

• R. E. Carhart, H. D. Cash, J. F. Moore:
  StrateGene: object-oriented programming in molecular biology. 3-9
  
• Eugene W. Myers, Webb Miller:
  Optimal alignments in linear space. 11-17
  
• Gad M. Landau, Uzi Vishkin, Ruth Nussinov:
  Locating alignments with k differences for nucleotide and amino acid sequences. 19-24
  
• C. B. Lawrence, D. A. Goldman:
  Definition and identification of homology domains. 25-33
  
• J. D. Hall, Eugene W. Myers:
  A software tool for finding locally optimal alignments in protein and nucleic acid sequences. 35-40
  
• Samuel Karlin, Macdonald Morris, G. Ghandour, M.-Y. Leung:
  Algorithms for identifying local molecular sequence features. 41-51
  
• Rodger Staden:
  Methods to define and locate patterns of motifs in sequences. 53-60
  
• Michael Gribskov, M. Homyak, J. Edenfield, David Eisenberg:
  Profile scanning for three-dimensional structural patterns in protein sequences. 61-66
  
• J. F. Collins, A. F. W. Coulson, A. Lyall:
  The significance of protein sequence similarities. 67-71
  
• J. Owens, D. Chatterjee, Ruth Nussinov, Andrzej K. Konopka, Jacob V. Maizel:
  A fixed-point alignment technique for detection of recurrent and common sequence motifs associated with biological features. 73-77
  
• U. Grob, K. Stuber:
  Recognition of ill-defined signals in nucleic acid sequences. 79-88
  
• Mauno Vihinen:
  An algorithm for simultaneous comparison of several sequences. 89-92
  
• U. Melcher:
  A readable and space-efficient DNA sequence representation: application to caulimoviral DNAs. 93-96
  
• Lloyd Allison, Chut N. Yee:
  Restriction site mapping is in separation theory. 97-101
  
• Pierre Tufféry, Philippe Dessen, C. Mugnier, Serge A. Hazout:
  Restriction map construction using a 'complete sentences compatibility' algorithm. 103-110
  
• B. Bellon:
  Construction of restriction maps. 111-115
  
• Trevor I. Dix, Dorota H. Kieronska:
  Errors between sites in restriction site mapping. 117-123
  
• J. Sulston, F. Mallett, Rodger Staden, R. Durbin, Terry Horsnell, A. Coulson:
  Software for genome mapping by fingerprinting techniques. 125-132
  
• Wilma K. Olson, Annankoil R. Srinivasan:
  The translation of DNA primary base sequence into three-dimensional structure. 133-142
  
• Robert Cedergren, Daniel Gautheret, Guy Lapalme, François Major:
  A secondary and tertiary structure editor for nucleic acids. 143-146
  
• R. K. Tan, M. Prabhakaran, C. S. Tung, Stephen C. Harvey:
  AUGUR: a program to predict, display and analyze the tertiary structure of B-DNA. 147-151
  
• Shu-Yun Le, Jih-H. Chen, Kathleen M. Currey, Jacob V. Maizel:
  A program for predicting significant RNA secondary structures. 153-159
  
• J. L. Modelevsky, T. G. Akers:
  Reiterative RNA folding and occupancy rate analysis for mRNA modelling. 161-166
  
• Robert E. Bruccoleri, G. Heinrich:
  An improved algorithm for nucleic acid secondary structure display. 167-173
  
• R. J. Folz, J. I. Gordon:
  PARA-SITE: a computer algorithm for rapidly analyzing the physical- chemical properties of amino acid sequences at sites of co- and post- translational protein processing. 175-179
  
• B. A. Jameson, H. Wolf:
  The antigenic index: a novel algorithm for predicting antigenic determinants. 181-186
  
• H. Wolf, S. Modrow, M. Motz, B. A. Jameson, G. Hermann, B. Fortsch:
  An integrated family of amino acid sequence analysis programs. 187-191
  
• D. Shalloway, S. F. Sneddon, E. K. Little:
  Microcomputer-based three-dimensional stereoscopic macromolecular graphics display. 193-196
  
• J. A. Bossinger:
  The Annotator's Assistant: an expert system for direct submission of genetic sequence data. 197-202
  
• T. P. Keenan, Stephen A. Krawetz:
  Computer video acquisition and analysis system for biological data. 203-210
  
• K. M. Williams:
  Version 5 of the Mount-Conrad-Myers Sequence Analysis Software Package now available. 211
  
• D. W. Smith:
  A complete, yet flexible, system for DNA/protein sequence analysis using VAX/VMS computers. 212
  
• T. Friedemann:
  Alignment of multiple DNA and protein sequence data. 213-214
  
• J. Campione-Piccardo, R. Moro:
  Modification of DNA ends and detection of restriction enzyme recognition sequences in their ligated junctions. 215-216
  
• Edmond J. Breen, Lois H. Browne, Len Glue, Keith L. Williams:
  The DNA rodent: a portable hand held DNA sequence reader. 217
  
• H. B. Jenson:
  Enhancement of DNA sequence computer programs by using digitized voice output. 218-232
  

Volume 4, Number 2, April 1988

• E. B. Moser, A. M. Saxton, J. P. Geaghan:
  Biological applications of the SAS system: an overview. 233-238
  
• G. F. Griffin, G. N. Bastin:
  Hand-held computer program for field-capture and analysis of herbage yield and composition data using a modified dry-weight-rank and yield estimate method. 239-242
  
• Karl Sirotkin:
  A computer program to display codon changes caused by mutagenesis. 243-247
  
• A. Mynett:
  FUGE: an analytical ultracentrifuge simulation for teaching purposes. 249-252
  
• J. L. Modelevsky, T. G. Akers:
  BCE: a tool for software integration. 253-257
  
• J. Campione-Piccardo:
  Algorithms for determining the fate of sites and domain boundaries in computer simulations of recombinant DNA procedures. 259-264
  
• Pasquale Petrilli:
  PROSOFT: a general purpose software in protein chemistry. 265-270
  
• C. D. Porter, A. G. Porter, L. C. Archard:
  BBC microcomputer controlled field inversion gel electrophoresis. 271-273
  
• J. D. Santangelo:
  A general purpose computer analysis system for chromatographic data. 275-279
  
• W. Vanden Berghe, P. Aerts:
  A hidden-line algorithm for graphical reconstruction of serially sectioned objects. 281-289
  
• M. A. Fernandes, P. J. Jackman, S. A. Clark, S. R. Gunard:
  Detection and quantification of microorganisms in a heterogeneous foodstuff by image analysis. 291-295
  
• J. Mrazek, J. Kypr:
  Computer program Jamsek combining statistical and stereochemical rules for the prediction of protein secondary structure. 297-302
  
• Francesco Facchiano, Antonio Facchiano, R. Ragone, Giovanni Colonna:
  New graphic representation of structural parameters of proteins. 303-305
  
• Joaquín Dopazo:
  Reducing the effect of the data order in algorithms for constructing phylogenetic trees. 307
  
• J. L. Modelevsky, T. G. Akers:
  3-D multi-variate data display tool as a protein design aid. 308
  
• J. Mandler:
  HYSTRUC: hydropathy and secondary structure prediction. 309
  
• J. Mandler:
  BETRA: a helpful tool for Beckman Microgenie users. 310-330
  

Volume 4, Number 3, August 1988

• G. W. Kidder III:
  Resolution improvement by modulation of analog-to-digital converters. 331-335
  
• Shu-Yun Le, Jih-H. Chen, Ruth Nussinov, Jacob V. Maizel:
  An improved secondary structure computation method and its application to intervening sequence in the human alpha-likeglobin mRNA precursors. 337-344
  
• D. R. Boswell:
  A program for template matching of protein sequences. 345-350
  
• Gilbert Deléage, F. F. Clerc, B. Roux, D. C. Gautheron:
  ANTHEPROT: a package for protein sequence analysis using a microcomputer. 351-356
  
• Olivier Gascuel, J. L. Golmard:
  A simple method for predicting the secondary structure of globular proteins: implications and accuracy. 357-365
  
• K. Nakata, M. Kanehisa, Jacob V. Maizel:
  Discriminant analysis of promoter regions in Escherichia coli sequences. 367-371
  
• R. P. Shellis:
  A microcomputer program to evaluate the saturation of complex solutions with respect to biominerals. 373-379
  
• Modesto Orozco, F. Javier Luque:
  POEMS: program for outliers elimination in multidimensional space. 381-385
  
• Bruce A. Shapiro:
  An algorithm for comparing multiple RNA secondary structures. 387-393
  
• A. H. Reisner, C. A. Bucholtz:
  The use of various properties of amino acids in color and monochrome dot-matrix analyses for protein homologies. 395-402
  
• A. Fielding:
  Matrix algebra routines for the Acorn Archimedes microcomputer: example applications. 403-404
  
• A. M. Popowicz, P. F. Dash:
  SIGSEQ: a computer program for predicting signal sequence cleavage sites. 405-406
  
• C. Bergmann, R. Bergmann:
  SCATTER: a program to correct UV spectra recorded with an LKB Ultrospec interfaced to an Apple IIe for light scattering by particles or aggregates. 407
  
• J. M. Smith:
  CELLBASE: a database management system for the control of cell line storage. 408-430
  

Volume 4, Number 4, November 1988

• A. Jimenez-Sanchez, E. C. Guzman:
  Direct procedure for the determination of the number of replication forks and the reinitiation fraction in bacteria. 431-433
  
• M. Equihua:
  Analysis of finite mixture of distributions: a statistical tool for biological classification problems. 435-440
  
• P. Taylor:
  A program for drawing evolutionary trees. 441-443
  
• François Major, R. Feldmann, Guy Lapalme, Robert Cedergren:
  FUS: a system to simulate conformational changes in biological macromolecules. 445-451
  
• Marie-Odile Delorme, Alain Hénaut:
  Merging of distance matrices and classification by dynamic clustering. 453-458
  
• R. Smith:
  A finite state machine algorithm for finding restriction sites and other pattern matching applications. 459-465
  
• K. Tajima:
  Multiple DNA and protein sequence alignment on a workstation and a supercomputer. 467-471
  
• Stavros J. Hamodrakas:
  A protein secondary structure prediction scheme for the IBM PC and compatibles. 473-477
  
• L. Menendez-Arias, J. Gomez-Gutierrez, M. Garcia-Ferrandez, A. Garcia-Tejedor, F. Moran:
  A BASIC microcomputer program to calculate the secondary structure of proteins from their circular dichroism spectrum. 479-482
  
• F. Dardel, P. Bensoussan:
  DNAid: a Macintosh full screen editor featuring a built-in regular expression interpreter for the search of specific patterns in biological sequences using finite state automata. 483-486
  
• R. J. Beynon:
  A Macintosh Hypercard stack for calculation of thermodynamically- corrected buffer recipes. 487-490
  
• W. Bains:
  AXE: a program for isolating short segments of long DNA sequences. 491-492
  
• J. Mandler:
  ANTIGEN: protein surface residue prediction. 493
  

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