Computer Applications in the Biosciences, Volume 13

Volume 13, Number 1, February 1997

• 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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