Journal: Bioinformatics

Volume 11, Issue 6

577 -- 581D. Bordo. Comparison of side chain interactions performed by structurally equivalent residues in homologous protein structures
583 -- 589Andrey A. Ptitsyn, Dmitry A. Grigorovich. Object-oriented data handler for sequence analysis software development
591 -- 593S. Sudarsanam, S. Srinivasan. Searching for protein loops in parallel
595 -- 602D. J. Brown. A qualitative ecological model to support mariculture pond water quality management
603 -- 613J. D. Parsons. Improved tools for DNA comparison and clustering
615 -- 619J. D. Parsons. Miropeats: graphical DNA sequence comparisons
621 -- 625Julio Rozas, Ricardo Rozas. DnaSP, DNA sequence polymorphism: an interactive program for estimating population genetics parameters from DNA sequence data
627 -- 632D. S. Tuckwell, M. J. Humphries, Andy Brass. Protein secondary structure prediction by the analysis of variation and conservation in multiple alignments
633 -- 644Mark Gerstein, Russ B. Altman. Using a measure of structural variation to define a core for the globins
645 -- 655Carol Soderlund, I. Dunham. SAM: a system for iteratively building marker maps
667 -- 673Richard Blevins, Jeffery S. Aaronson, J. Myerson, G. Hamm, K. O. Elliston. PROFILER: a tool for automatic searching of internally maintained databases
675 -- 679D. L. Hoffman, S. Laiter, Raj K. Singh, Iosif I. Vaisman, Alexander Tropsha. Rapid protein structure classification using one-dimensional structure profiles on the bioSCAN parallel computer
681 -- 684Christophe Geourjon, Gilbert Deléage. SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments
685 -- 692A. Nakaya, K. Yamamoto, Akinori Yonezawa. RNA secondary structure prediction using highly parallel computers

Volume 11, Issue 5

469 -- 475F. Fournet, F. Hospital, J. M. Elsen. A FORTRAN program to simulate the evolution of genetic variability in a small population
477 -- 488Y. V. Kondrakhin, Alexander E. Kel, Nikolay A. Kolchanov, Aida G. Romashchenko, Luciano Milanesi. Eukaryotic promoter recognition by binding sites for transcription factors
489 -- 495Stéphane Audic, G. Zanetti. Automatic reading of hybridization filter images
497 -- 501Y. Cai, C. Chen. Artificial neural network method for discriminating coding regions of eukaryotic genes
503 -- 507P. M. Leong, S. Morgenthaler. Random walk and gap plots of DNA sequences
509 -- 515Arlin Stoltzfus, D. F. Spencer, W. F. Doolittle. Methods for evaluating exon-protein correspondences
517 -- 534Wolfgang Wiechert, B. Joksch, R. Wittig, A. Hartbrich, T. Höner, M. Möllney. Object-oriented programming for the biosciences
535 -- 540G. F. Weiller, A. Gibbs. DIPLOMO: the tool for a new type of evolutionary analysis
541 -- 0Mikhail S. Gelfand. FANS-REF: a bibliography on statistics and functional analysis of nucleotide sequences
543 -- 551Osamu Gotoh. A weighting system and algorithm for aligning many phylogenetically related sequences
553 -- 556Patrick Nitschké, Isabelle Pignot-Paintrand, Francine Iftode, Hervé Delacroix. DEFPARAM: a program package for aligning elliptical sections of biological objects containing an n-fold symmetry
557 -- 56Victor B. Strelets, Hwa A. Lim. Compression of protein sequence databases
563 -- 566Q. K. Chen, G. Z. Hertz, Gary D. Stormo. MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices
567 -- 569Dónall A. Mac Dónaill. On the application of integer arithmetic in nucleotide sequence analysis
571 -- 573Roger A. Sayle, Mansoor A. S. Saqi, M. Weir, Andrew Lyall. PdbAlign, PdbDist and DistAlign: tools to aid in relating sequence variability to structure

Volume 11, Issue 4

339 -- 347S. Schweigert, P. V. Herde, Peter R. Sibbald. Issues in incorporation semantic integrity in molecular biological object-oriented databases
349 -- 359Khawaja Sirajuddin, Tomomasa Nagashima, Koichi Ono. A new algorithm for predicting splice site sequence based on an improvement of categorical discriminant analysis
361 -- 371S. W. Humphries, S. P. Long. WIMOVAC: a software package for modelling the dynamics of plant leaf and canopy photosynthesis
373 -- 378Salvatore Lanzavecchia, L. Tosoni, Pier Luigi Bellon. Three-dimensional reconstruction of helical structures with fast inversion of very large Fourier transforms
379 -- 387Y. M. Fraenkel, Y. Mandel, D. Friedberg, Hanah Margalit. Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon
389 -- 397A. M. Chen, J. N. Lucas, F. S. Hill, David J. Brenner, Rainer K. Sachs. Chromosome aberrations produced by ionizing radiation: Monte Carlo simulations and chromosome painting data
399 -- 411Hiroshi Mamitsuka, Kenji Yamanishi. alpha-Helix region prediction with stochastic rule learning
413 -- 422Hiroshi Mamitsuka. Representing inter-residue dependencies in protein sequences with probabilistic networks
423 -- 426N. N. Nazipova, Svetlana A. Shabalina, Aleksey Y. Ogurtsov, Alexey S. Kondrashov, Mikhail A. Roytberg, G. V. Buryakov, S. E. Vernoslov. SAMSON: a software package for the biopolymer primary structure analysis
427 -- 434Jorge Fernandez-de-Cossio, J. Gonzalez, Vladimir Besada. A computer program to aid the sequencing of peptides in collision- activated decomposition experiments
435 -- 439. SUBIM: a program for analysing the Kabat database and determining the variability subgroup of a new immunoglobulin sequence
441 -- 447M. G. Claros. MitoProt, a Macintosh application for studying mitochondrial proteins
449 -- 455Jürgen Kleffe, Klaus Hermann, W. Gunia, W. Vahrson, Burghardt Wittig. DNASTAT: a Pascal unit for the statistical analysis of DNA and protein sequences
457 -- 462Olga D. Ermolaeva, M. C. Wagner. SUBTRACT: a computer program for modeling the process of subtractive hydridization

Volume 11, Issue 3

229 -- 235Richard M. Karp, Lee Aaron Newberg. An algorithm for analysing probed partial digestion experiments
237 -- 246Sungwon Jung, Steve Perkins, Yang Zhong, Sakti Pramanik, John H. Beaman. A new data model for biological classification
247 -- 251A. Purvis, Andrew Rambaut. Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data
253 -- 260Francesco Vivarelli, G. Giusti, M. Villani, Renato Campanini, Piero Fariselli, Mario Compiani, Rita Casadio. LGANN: a parallel system combining a local genetic algorithm and neural networks for the prediction of secondary structure of proteins
261 -- 272H. Cantalloube, Gilles Labesse, Jacques Chomilier, C. Nahum, Y. Y. Cho, V. Chams, A. Achour, A. Lachgar, J. P. Mbika, W. Issing. Automat and BLAST: comparison of two protein sequence similarity search programs
273 -- 279C. Fondrat, Philippe Dessen. A rapid access motif database (RAMdb) with a search algorithm for the retrieval patterns in nucleic acids or protein databanks
281 -- 287M. Bansal, D. Bhattacharyya, B. Ravi. NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures
289 -- 292M. Bansal, D. Bhattacharyya, S. Vijaylakshmi. NUVIEW: software for display and interactive manipulation of nucleic acid models
293 -- 300T. M. Nair, Sanjeev S. Tambe, Bhaskar D. Kulkarni. Analysis of transcription control signals using artificial neural networks
301 -- 308Oswaldo Trelles-Salazar, Emilio L. Zapata, Joaquín Dopazo, A. F. Coulson, José María Carazo. An image-processing approach to dotplots: an X-Window-based program for interactive analysis of dotplots derived from sequence and structural data
309 -- 315Martin Reczko, Artemis G. Hatzigeorgiou, Niels Mache, Andreas Zell, Sándor Suhai. A parallel neural network simulator on the connection machine CM-5
317 -- 319Gautam B. Singh, Stephen A. Krawetz. DNAView: a quality assessment tool for the visualization of large sequenced regions
321 -- 329Jean Thioulouse, J. R. Lobry. Co-inertia analysis of amino-acid physico-chemical properties and protein composition with the ADE package
331 -- 335Andrey A. Mironov, N. N. Alexandrov, N. Yu. Bogodarova, A. Grigorjev, V. F. Lebedev, L. V. Lunovskaya, M. E. Truchan, Pavel A. Pevzner. DNASUN: a package of computer programs for the biotechnology laboratory

Volume 11, Issue 2

117 -- 124Ying Xu, Richard J. Mural, Edward C. Uberbacher. Correcting sequencing errors in DNA coding regions using a dynamic programming approach
125 -- 131K. Nakata. Prediction of zinc finger DNA binding protein
141 -- 145A. Perrakis, C. Constantinides, A. Athanasiades, Stavros J. Hamodrakas. PBM: a software package to create, display and manipulate interactively models of small molecules and proteins on IBM-compatible PCs
147 -- 153Kun-Mao Chao, Jinghui Zhang, James Ostell, Webb Miller. A local alignment tool for very long DNA sequences
155 -- 157G. D. Smith, K. E. Bernstein. BULLET: a computer simulation of shotgun DNA sequencing
159 -- 166Hidemi Watanabe, Jinya Otsuka. A comprehensive representation of extensive similarity linkage between large numbers of proteins
167 -- 171Carlo Nesti, Giorgio Poli, Milvia Chicca, Piera Ambrosino, Chiara Scapoli, Italo Barrai. Phylogeny inferred from codon usage pattern in 31 organisms
173 -- 179E. Veklerov, C. H. Martin, E. H. Theil. TRAMP: a software package for generating transposon maps
181 -- 186Julie Dawn Thompson. Introducing variable gap penalties to sequence alignment in linear space
187 -- 194M. L. Metzker, K. M. Allain, Richard A. Gibbs. Accurate determination of DNA in agarose gels using the novel algorithm GelScann(1.0)
195 -- 199J. Mrazek, J. Kypr. Middle-range clustering of nucleotides in genomes
201 -- 207M. Ehlde, G. Zacchi. MIST: a user-friendly metabolic simulator
209 -- 212Juncai Ma, Satoru Miyazaki, Hideaki Sugawara. A handy database for culture collections worldwide: CCINFO-PC
213 -- 218O. E. Belova, V. A. Likhoshvai, S. I. Bazhan, Vitaly A. Kulichkov. A computer system for analysis and integrated description of regulation of the molecular-genetic system of interferon induction and action
219 -- 223Reinhard Doelz, F. Eggenberger. A compression mechanism for sequence databases to improve the efficiency of conventional tools
224 -- 226Reinhard Doelz. Optimal production of biological documentation: the JAM format

Volume 11, Issue 1

3 -- 6A. Julich. Implementations of BLAST for parallel computers
13 -- 18Makoto Hirosawa, Yasushi Totoki, Masaki Hoshida, Masato Ishikawa. Comprehensive study on iterative algorithms of multiple sequence alignment
19 -- 27J. F. Wright, D. R. Morse, G. M. Tardivel. An investigation into the use of hypertext as a user interface to taxonomic keys
29 -- 37E. Granjeon, Philippe Tarroux. Detection of compositional constraints in nucleic acid sequences using neural networks
39 -- 44A. M. Eroshkin, V. I. Fomin, P. A. Zhilkin, V. V. Ivanisenko, Y. V. Kondrakhin. PROANAL version 2: multifunctional program for analysis of multiple protein sequence alignments and for studying the structure--activity relationships in protein families
49 -- 57Hans Leo Bodlaender, Rodney G. Downey, Michael R. Fellows, Michael T. Hallett, Harold T. Wareham. Parameterized complexity analysis in computational biology
59 -- 70Marie-France Sagot, Alain Viari, Joël Pothier, Henry Soldano. Finding flexible patterns in a text: an application to three-dimensional molecular matching
71 -- 86Dinesh Manocha, Yunshan Zhu, William V. Wright. Conformational analysis of molecular chains using nano-kinematics
87 -- 99Bilha Sandak, Ruth Nussinov, Haim J. Wolfson. An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching
101 -- 109J. Perochon-Dorisse, Farid Chetouani, S. Aurel, N. Iscolo, B. Michot. RNA-d2: a computer program for editing and display of RNA secondary structures
111 -- 115M. Schoniger, Arndt von Haeseler. Simulating efficiently the evolution of DNA sequences