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ORCIDComputer Applications in the Biosciences, Volume 11
Volume 11, Number 1, February 1995
- A. Julich:
Implementations of BLAST for parallel computers. 3-6 - S. M. Resenchuk, V. M. Blinov:
ALIGNMENT SERVICE: creation and processing of alignments of sequences of unlimited length. 7-11 - Makoto Hirosawa, Yasushi Totoki, Masaki Hoshida, Masato Ishikawa:
Comprehensive study on iterative algorithms of multiple sequence alignment. 13-18 - J. F. Wright, D. R. Morse, G. M. Tardivel:
An investigation into the use of hypertext as a user interface to taxonomic keys. 19-27 - E. Granjeon, Philippe Tarroux:
Detection of compositional constraints in nucleic acid sequences using neural networks. 29-37 - A. M. Eroshkin, V. I. Fomin, P. A. Zhilkin, V. V. Ivanisenko, Yury V. Kondrakhin:
PROANAL version 2: multifunctional program for analysis of multiple protein sequence alignments and for studying the structure--activity relationships in protein families. 39-44 - O. White, W. FitzHugh:
A rapid retrieval tool for operating on large, flat archive files. 45-47 - Hans L. Bodlaender
, Rodney G. Downey, Michael R. Fellows, Michael T. Hallett, Harold T. Wareham:
Parameterized complexity analysis in computational biology. 49-57 - Marie-France Sagot, Alain Viari, Joël Pothier, Henry Soldano:
Finding flexible patterns in a text: an application to three-dimensional molecular matching. 59-70 - Dinesh Manocha, Yunshan Zhu, William V. Wright:
Conformational analysis of molecular chains using nano-kinematics. 71-86 - Bilha Sandak, Ruth Nussinov, Haim J. Wolfson:
An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching. 87-99 - J. Perochon-Dorisse, Farid Chetouani, S. Aurel, N. Iscolo, B. Michot:
RNA-d2: a computer program for editing and display of RNA secondary structures. 101-109 - M. Schoniger, Arndt von Haeseler:
Simulating efficiently the evolution of DNA sequences. 111-115
Volume 11, Number 2, April 1995
- Ying Xu, Richard J. Mural, Edward C. Uberbacher:
Correcting sequencing errors in DNA coding regions using a dynamic programming approach. 117-124 - Kotoko Nakata:
Prediction of zinc finger DNA binding protein. 125-131 - M. Ligr, C. Ron, L. Natr:
Calculation of the photoperiod length. 133-139 - Anastassis 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. 141-145 - Kun-Mao Chao, Jinghui Zhang, James Ostell, Webb Miller:
A local alignment tool for very long DNA sequences. 147-153 - G. D. Smith, K. E. Bernstein:
BULLET: a computer simulation of shotgun DNA sequencing. 155-157 - Hidemi Watanabe, Jinya Otsuka:
A comprehensive representation of extensive similarity linkage between large numbers of proteins. 159-166 - Carlo Nesti, Giorgio Poli, Milvia Chicca, Piera Ambrosino, Chiara Scapoli, Italo Barrai:
Phylogeny inferred from codon usage pattern in 31 organisms. 167-171 - Eugene Veklerov, Christopher H. Martin, Edward H. Theil:
TRAMP: a software package for generating transposon maps. 173-179 - Julie Dawn Thompson:
Introducing variable gap penalties to sequence alignment in linear space. 181-186 - Michael L. Metzker, Kyle M. Allain, Richard A. Gibbs:
Accurate determination of DNA in agarose gels using the novel algorithm GelScann(1.0). 187-194 - Jan Mrázek, J. Kypr:
Middle-range clustering of nucleotides in genomes. 195-199 - M. Ehlde, G. Zacchi:
MIST: a user-friendly metabolic simulator. 201-207 - Juncai Ma, Satoru Miyazaki, Hideaki Sugawara:
A handy database for culture collections worldwide: CCINFO-PC. 209-212 - O. 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. 213-218 - Reinhard Doelz, F. Eggenberger:
A compression mechanism for sequence databases to improve the efficiency of conventional tools. 219-223 - Reinhard Doelz:
Optimal production of biological documentation: the JAM format. 224-226
Volume 11, Number 3, June 1995
- Richard M. Karp, Lee Aaron Newberg:
An algorithm for analysing probed partial digestion experiments. 229-235 - Sungwon Jung, Steve Perkins, Yang Zhong, Sakti Pramanik, John H. Beaman:
A new data model for biological classification. 237-246 - Andy Purvis, Andrew Rambaut:
Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. 247-251 - Francesco Vivarelli, G. Giusti, Marco 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. 253-260 - Hubert Cantalloube, Gilles Labesse, Jacques Chomilier, Carole E. 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. 261-272 - C. Fondrat, Philippe Dessen:
A rapid access motif database (RAMdb) with a search algorithm for the retrieval patterns in nucleic acids or protein databanks. 273-279 - Manju Bansal, Dhananjay Bhattacharyya, B. Ravi:
NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. 281-287 - Manju Bansal, Dhananjay Bhattacharyya, S. Vijaylakshmi:
NUVIEW: software for display and interactive manipulation of nucleic acid models. 289-292 - T. M. Nair, Sanjeev S. Tambe, Bhaskar D. Kulkarni:
Analysis of transcription control signals using artificial neural networks. 293-300 - Oswaldo 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. 301-308 - Martin Reczko, Artemis G. Hatzigeorgiou, Niels Mache, Andreas Zell, Sándor Suhai:
A parallel neural network simulator on the connection machine CM-5. 309-315 - Gautam B. Singh, Stephen A. Krawetz:
DNAView: a quality assessment tool for the visualization of large sequenced regions. 317-319 - Jean Thioulouse, J. R. Lobry:
Co-inertia analysis of amino-acid physico-chemical properties and protein composition with the ADE package. 321-329 - Andrey 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. 331-335
Volume 11, Number 4, August 1995
- S. Schweigert, P. V. Herde, Peter R. Sibbald:
Issues in incorporation semantic integrity in molecular biological object-oriented databases. 339-347 - Khawaja Sirajuddin, Tomomasa Nagashima, Koichi Ono:
A new algorithm for predicting splice site sequence based on an improvement of categorical discriminant analysis. 349-359 - S. W. Humphries, S. P. Long:
WIMOVAC: a software package for modelling the dynamics of plant leaf and canopy photosynthesis. 361-371 - Salvatore Lanzavecchia, L. Tosoni, Pier Luigi Bellon:
Three-dimensional reconstruction of helical structures with fast inversion of very large Fourier transforms. 373-378 - Y. M. Fraenkel, Y. Mandel, D. Friedberg, Hanah Margalit:
Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon. 379-387 - Allen M. Chen, Joe N. Lucas, Francesca S. Hill, David J. Brenner, Rainer K. Sachs:
Chromosome aberrations produced by ionizing radiation: Monte Carlo simulations and chromosome painting data. 389-397 - Hiroshi Mamitsuka, Kenji Yamanishi:
alpha-Helix region prediction with stochastic rule learning. 399-411 - Hiroshi Mamitsuka:
Representing inter-residue dependencies in protein sequences with probabilistic networks. 413-422 - Nafisa 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. 423-426 - Jorge Fernandez-de-Cossío, Luis Javier González, Vladimir Besada:
A computer program to aid the sequencing of peptides in collision- activated decomposition experiments. 427-434 - S. Deret, C. Maissiat, P. Aucouturier, Jacques Chomilier:
SUBIM: a program for analysing the Kabat database and determining the variability subgroup of a new immunoglobulin sequence. 435-439 - M. Gonzalo Claros:
MitoProt, a Macintosh application for studying mitochondrial proteins. 441-447 - Jürgen Kleffe, Klaus Hermann, W. Gunia, Wolfgang Vahrson, Burghardt Wittig:
DNASTAT: a Pascal unit for the statistical analysis of DNA and protein sequences. 449-455 - Olga D. Ermolaeva, M. C. Wagner:
SUBTRACT: a computer program for modeling the process of subtractive hydridization. 457-462
Volume 11, Number 5, October 1995
- M. E. Drets, G. A. Drets, P. J. Queirolo, F. J. Monteverde:
Computer graphics as a tool in cytogenetic research and education. 463-468 - F. Fournet, Frédéric Hospital, J. M. Elsen:
A FORTRAN program to simulate the evolution of genetic variability in a small population. 469-475 - Yury V. Kondrakhin, Alexander E. Kel, Nikolay A. Kolchanov, Aida G. Romashchenko, Luciano Milanesi:
Eukaryotic promoter recognition by binding sites for transcription factors. 477-488 - Stéphane Audic, Gianluigi Zanetti:
Automatic reading of hybridization filter images. 489-495 - Yudong Cai, Changqing Chen:
Artificial neural network method for discriminating coding regions of eukaryotic genes. 497-501 - P. M. Leong, Stephan Morgenthaler:
Random walk and gap plots of DNA sequences. 503-507 - Arlin Stoltzfus, D. F. Spencer, W. Ford Doolittle:
Methods for evaluating exon-protein correspondences. 509-515 - Wolfgang Wiechert, B. Joksch, R. Wittig, A. Hartbrich, T. Höner, Michael Möllney:
Object-oriented programming for the biosciences. 517-534 - Georg F. Weiller, Adrian J. Gibbs:
DIPLOMO: the tool for a new type of evolutionary analysis. 535-540 - Mikhail S. Gelfand:
FANS-REF: a bibliography on statistics and functional analysis of nucleotide sequences. 541 - Osamu Gotoh:
A weighting system and algorithm for aligning many phylogenetically related sequences. 543-551 - Patrick Nitschké, Isabelle Pignot-Paintrand, Francine Iftode, Hervé Delacroix:
DEFPARAM: a program package for aligning elliptical sections of biological objects containing an n-fold symmetry. 553-556 - Victor B. Strelets, Hwa A. Lim:
Compression of protein sequence databases. 557-56 - Q. 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. 563-566 - Dónall A. Mac Dónaill:
On the application of integer arithmetic in nucleotide sequence analysis. 567-569 - Roger A. Sayle, Mansoor A. S. Saqi, M. Weir, Andrew Lyall:
PdbAlign, PdbDist and DistAlign: tools to aid in relating sequence variability to structure. 571-573
Volume 11, Number 6, December 1995
- D. Bordo:
Comparison of side chain interactions performed by structurally equivalent residues in homologous protein structures. 577-581 - Andrey A. Ptitsyn, Dmitry A. Grigorovich:
Object-oriented data handler for sequence analysis software development. 583-589 - Sucha Sudarsanam, Subhashini Srinivasan:
Searching for protein loops in parallel. 591-593 - D. J. Brown:
A qualitative ecological model to support mariculture pond water quality management. 595-602 - J. D. Parsons:
Improved tools for DNA comparison and clustering. 603-613 - J. D. Parsons:
Miropeats: graphical DNA sequence comparisons. 615-619 - Julio Rozas, Ricardo Rozas:
DnaSP, DNA sequence polymorphism: an interactive program for estimating population genetics parameters from DNA sequence data. 621-625 - D. S. Tuckwell, M. J. Humphries, Andy Brass:
Protein secondary structure prediction by the analysis of variation and conservation in multiple alignments. 627-632 - Mark Gerstein, Russ B. Altman:
Using a measure of structural variation to define a core for the globins. 633-644 - Carol Soderlund, I. Dunham:
SAM: a system for iteratively building marker maps. 645-655 - Pascal R. R. Courtois, Maurice L. J. Moncany:
A probabilistic algorithm for interactive huge genome comparison. 657-665 - Richard Blevins, Jeffery S. Aaronson, Joseph Myerson, Greg Hamm, Keith O. Elliston:
PROFILER: a tool for automatic searching of internally maintained databases. 667-673 - D. 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. 675-679 - Christophe Geourjon, Gilbert Deléage:
SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. 681-684 - Akihiro Nakaya, Kenji Yamamoto, Akinori Yonezawa:
RNA secondary structure prediction using highly parallel computers. 685-692
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