Computer Applications in the Biosciences, Volume 9
Volume 9, Number 1, February 1993
- M. Suyama, A. Ogiwara, Takaaki Nishioka, J. Oda: Searching for amino acid sequence motifs among enzymes: the Enzyme- Reaction Database. 9-15
- Victor V. Solovyev, Kira S. Makarova: A novel method of protein sequence classification based on oligopeptide frequency analysis and its application to search for functional sites and to domain localization. 17-24
- D. Krishna, P. J. Reddy: Microcomputer BASIC programs for rapid determination of lethal dosages of biocides using logit transformations. 29-35
- L. Lemesle-Varloot, C. Gaboriaud, A. Morgat, G. Pantel, J. P. Mornon, S. Lavaitte, F. Lestang, B. Henrissat: MANSEK and SUNHCA. Two interactive programs for the hydrophobic cluster analysis of protein sequences. 37-44
- M. Hauer-Jensen: Sample size calculation, power analysis and randomization: research project design in Windows. 45-47
- Thure Etzold, P. Argos: Transforming a set of biological flat file libraries to a fast access network. 59-64
- R. Schuster, Stefan Schuster: Refined algorithm and computer program for calculating all non-negative fluxes admissible in steady states of biochemical reaction systems with or without some flux rates fixed. 79-85
- Christophe Geourjon, Gilbert Deléage: Interactive and graphic coupling between multiple alignments, secondary structure predictions and motif/pattern scanning into proteins. 87-91
- Valerio Balzarotti, V. Colizzi, S. Morante, Valerio Parisi: An algorithm for the identification of similar oligopeptides between amino acid sequences. 93-100
- Joaquín Dopazo, A. Taberner, A. Moya: Quantitative characterization of antigens using monoclonal antibody reactivities. 101-107
- G. H. Dibdin: Short algorithm to compensate for sampling-volume errors in diffusion- cell studies. 109-111
- E. Wallin, C. Wettergren, F. Hedman, Gunnar von Heijne: Fast Needleman-Wunsch scanning of sequence databanks on a massively parallel computer. 117-118
Volume 9, Number 2, April 1993
- Joaquín Dopazo, A. Rodriguez, J. C. Saiz, F. Sobrino: Design of primers for PCR amplification of highly variable genomes. 123-125
- M. D. Delahunty, J. P. Mack: A general method of curve fitting and error analysis using a spreadsheet: determination of the binding constants of tight binding ligands in variable volume assays. 127-131
- J. E. Solomon, M. G. Harrington: A robust, high-sensitivity algorithm for automated detection of proteins in two-dimensional electrophoresis gels. 133-139
- Kiyoshi Asai, Satoru Hayamizu, Ken'ichi Handa: Prediction of protein secondary structure by the hidden Markov model. 141-146
- Y. Matsuo, Minoru Kanehisa: An approach to systematic detection of protein structural motifs. 153-159
- Makoto Hirosawa, Masaki Hoshida, Masato Ishikawa, Tomoyuki Toya: MASCOT: multiple alignment system for protein sequences based on three- way dynamic programming. 161-167
- Webb Miller: Building multiple alignments from pairwise alignments. 169-176
- Yves Van de Peer, Rupert De Wachter: TREECON: a software package for the construction and drawing of evolutionary trees. 177-182
- Claudine Landes, Alain Hénaut, Jean-Loup Risler: Dot-plot comparisons by multivariate analysis (DOCMA): a tool for classifying protein sequences. 191-196
- Gilbert Deléage, Christophe Geourjon: An interactive graphic program for calculating the secondary structure content of proteins from circular dichroism spectrum. 197-199
- A. Jamie Cuticchia, Jonathan Arnold, William E. Timberlake: PCAP: probe choice and analysis package - a set of programs to aid in choosing synthetic oligomers for contig mapping. 201-203
- Pasquale Petrilli: Classification of protein sequences by their dipeptide composition. 205-209
- B. K. Kiong, Tin Wee Tan: A hypertext-like approach to navigating through the GCG sequence analysis package. 211-214
- A. Jamie Cuticchia, Jonathan Arnold, William E. Timberlake: ODS: ordering DNA sequences - a physical mapping algorithm based on simulated annealing. 215-219
- Barry S. Fagin, J. Gill Watt, R. Gross: A special-purpose processor for gene sequence analysis. 221-226
- M. P. Mujumdar, C. K. Mitra: Electrogenic property of Na+, K(+)-ATPase through computer simulation. 227-230
Volume 9, Number 3, June 1993
- T. Karasawa, K. Tabuchi, M. Fumoto, T. Yasukawa: Development of simulation models for protein folding in a thermal annealing process - I: A simulation of BPTI folding by the pearl necklace model. 243-251
- Kenji Satou, Emiko Furuichi, Kyoko Takiguchi, Toshihisa Takagi, Satoru Kuhara: A deductive database system PACADE for analyzing 3-D and secondary structures of protein. 259-265
- Masato Ishikawa, Tomoyuki Toya, Masaki Hoshida, Katsumi Nitta, A. Ogiwara, Minoru Kanehisa: Multiple sequence alignment by parallel simulated annealing. 267-273
- Jürgen Kleffe, E. Grau: The joint distribution of patterns in random sequences with application to the RC-measure for expressivity. 275-283
- V. V. Panjukov: Finding steady alignments: similarity and distance. 285-290
- A. Z. Maksyutov, E. S. Zagrebelnaya: ADEPT: a computer program for prediction of protein antigenic determinants. 291-297
- T. Rouxel, Antoine Danchin, Alain Hénaut: METALGEN.DB: metabolism linked to the genome of Escherichia coli, a graphics-oriented database. 315-324
- A. D. Athanasiadis, A. A. Hatzopoulos, G. Theophilidis: A data-acquisition system for the analysis of the isometric tension generated by an electrically stimulated skeletal muscle. 325-330
- D. N. Nedde, Matthew O. Ward: Visualizing relationships between nucleic acid sequences using correlation images. 331-335
- D. W. Collins: FISH: a guide to protein-coding DNA sequences in the GenBank database. 337-342
- Christophe Lefèvre, Joh-E Ikeda: The position end-set tree: a small automaton for word recognition in biological sequences. 343-348
- Christophe Lefèvre, Joh-E Ikeda: Pattern recognition in DNA sequences and its application to consensus foot-printing. 349-354
- Osamu Gotoh: Optimal alignment between groups of sequences and its application to multiple sequence alignment. 361-370
- Hedvig Hegyi, Sándor Pongor: Predicting potential domain homologies from FASTA search results. 371-372
- Scott R. Presnell, Bruce I. Cohen, Fred E. Cohen: MacMatch: a tool for pattern-based protein secondary structure prediction. 373-374
- Edward S. Chen, C. Asano, Daniel B. Davison: Parallel alignment of DNA sequences on the Connection Machine CM-2. 375
Volume 9, Number 4, August 1993
- R. Heilig, M. Hausmann, W. Rens, J. A. Aten, C. Cremer: Time-optimized analysis of slit-scan chromosome profiles on a general- purpose personal computer. 381-385
- Kun-Mao Chao, Ross C. Hardison, Webb Miller: Locating well-conserved regions within a pairwise alignment. 387-396
- Shashank Date, Rajendra Kulkarni, Bhavna Kulkarni, Urmila Kulkarni-Kale, Ashok S. Kolaskar: Multiple alignment of sequences on parallel computers. 397-402
- P. R. Hunter: A numerical method for allocating microbial isolates to strain types when characterized by typing methods that are not 100% reproducible. 403-405
- Aleksandar Milosavljevic, Jerzy Jurka: Discovering simple DNA sequences by the algorithmic significance method. 407-411
- A. Howard: SCUM - simulation of cyanobacterial underwater movement. 413-419
- David B. Searls: Doing sequence analysis with your printer. 421-426
- Norihiro Sakamoto, Toshihisa Takagi, Yasubumi Sakaki: Development of the Overlapping Oligonucleotide Database and its application to signal sequence search of the human genome. 427-434
- E. S. Shpigelman, Edward N. Trifonov, Alexander Bolshoy: CURVATURE: software for the analysis of curved DNA. 435-440
- H. M. Sauro: SCAMP: a general-purpose simulator and metabolic control analysis program. 441-450
- A. Trubuil: Analysis of one-dimensional electrophoregrams. 451-458
- Hiroshi Dohi, Mitsuru Ishizuka, Shinsei Minoshima, Nobuyoshi Shimizu: GeneView: multi-language human gene mapping library with a graphical user interface. 459-464
- J. W. Brown: A toolkit for creating three-dimensional RNA pencil models. 465-467
- J. H. Nash: A computer program to calculate and design oligonucleotide primers from amino acid sequences. 469-471
- Z. Nesovic, George Harauz: 3DVISION: a program for display of three-dimensional wire models on a PC with VGA display. 472
- J. W. Brown: A Macintosh Hypercard compilation of small subunit ribosomal RNA sequences. 473
- G. Smutzer: A simple method for accessing and transferring nucleotide database files. 474
- W. X. Huang, M. I. Cohen, W. R. See: A fast graphics printing program for neurophysiological data. 475-476
- A. C. Pandey, M. V. Suryanarayana, R. K. Vishwakarma: A computer program in BASIC for estimation of LD50 of a chemical by Dixon's up and down method. 477-478
- J. M. Smith: OLIGOGET - a computerized database system for controlling oligonucleotide production. 479-480
Volume 9, Number 5, October 1993
- A. M. Eroshkin, P. A. Zhilkin, V. I. Fomin: Algorithm and computer program Pro_Anal for analysis of relationship between structure and activity in a family of proteins or peptides. 491-497
- Mark A. Shifman: PFGE MAPPER: a tool to aid in the analysis of pulse field gel electrophoresis maps. 511-515
- D. Yee, M. G. Prior, L. Z. Florence: Development of predictive models of laboratory animal growth using artificial neural networks. 517-522
- K. C. Yan, F. T. Chau: SCANGRAPH: a program for digitization of graphs using an image scanner. 531-534
- A. Taberner, P. Castanera, E. Silvestre, Joaquín Dopazo: Estimation of the intrinsic rate of natural increase and its error by both algebraic and resampling approaches. 535-540
- N. Prunella, Sabino Liuni, Marcella Attimonelli, Graziano Pesole: FASTPAT: a fast and efficient algorithm for string searching in DNA sequences. 541-545
- G. Landini, J. W. Rippin: Notes on the implementation of the mass-radius method of fractal dimension estimation. 547-550
- G. Muller, C. Gaspin, A. Etienne, E. Westhof: Automatic display of RNA secondary structures. 551-561
- Pedro Mendes: GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. 563-571
- Hermann-Georg Holzhütter, A. Schwendel, T. Grune, J. Quedenau, W. Siems: Estimation of steady-state flux rates in metabolic systems by computer simulations of radioactive tracer experiments. 573-580
- B. K. Kiong, Tin Wee Tan: A general UNIX interface for biocomputing and network information retrieval software. 581-586
- Rainer Fuchs: Block searches on VAX and Alpha computer systems. 587-591
- D. K. Green: Driving multiple pulsed field electrophoresis devices from one personal computer. 593-596
- P. L. Partner, M. L. Smith, W. Spoor, M. I. Clarkson: Computer simulation of selection in a hypothetical crop species. 597-605
- X. Salas, J. Portugal: PERFILS: a program for the quantitative treatment of footprinting data. 607-610
Volume 9, Number 6, December 1993
- Alexander E. Kel, Mikhail P. Ponomarenko, E. A. Likhachev, Yuri L. Orlov, I. V. Ischenko, Luciano Milanesi, Nikolay A. Kolchanov: SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites. 617-627
- V. M. Balcao, F. X. Malcata: STADEERS: a software package for the statistical design of experiments pertaining to the estimation of parameters in rate expressions that describe enzyme-catalyzed processes. 629-637
- D. Bordo: ENVIRON: a software package to compare protein three-dimensional structures with homologous sequences using local structural motifs. 639-645
- Chiara Scapoli, A. Rodriguez-Larralde, Stefano Volinia, Italo Barrai: Enrichment of oligonucleotide sets with transcription control signals. III: DNA from non-mammalian vertebrates. 647-651
- M. Edwards, Roger E. Cooley: Expertise in expert systems: knowledge acquisition for biological expert systems. 657-665
- M. T. Semertzidis, S. Deplanque, J. P. Mornon: OMEGA: a three-dimensional databank for protein structures (a complement to PDB). 667-670
- Edgardo A. Ferrán, Bernard Pflugfelder: A hybrid method to cluster protein sequences based on statistics and artificial neural networks. 671-680
- Salvatore Lanzavecchia, Pier Luigi Bellon, L. Tosoni: FT3D: three-dimensional Fourier analysis on small Unix workstations for electron microscopy and tomographic studies. 681-685
- F. Giuliano, Patrizio Arrigo, F. Scalia, Pasquale Paolo Cardo, G. Damiani: Potentially functional regions of nucleic acids recognized by a Kohonen's self-organizing map. 687-693
- Federico M. Stefanini, A. Camussi: APLOGEN: an object-oriented genetic algorithm performing Monte Carlo optimization. 695-700
- Sabino Liuni, N. Prunella, Graziano Pesole, Tiziana D'Orazio, Ettore Stella, Arcangelo Distante: SIMD parallelization of the WORDUP algorithm for detecting statistically significant patterns in DNA sequences. 701-707
- C. M. Henneke: Protein motif by computer: the perfect Greek key jellyroll designer. 709-722
- S. J. Taylor, R. A. Rastall, J. T. Sykes, S. C. Winter, C. Bucke: Primary sequence analysis and representation techniques in carbohydrates. 723-728
- Geoffrey J. Barton: An efficient algorithm to locate all locally optimal alignments between two sequences allowing for gaps. 729-734
- Peter De Rijk, Rupert De Wachter: DCSE, an interactive tool for sequence alignment and secondary structure research. 735-740
- M. O. Ortells, V. B. Cockcroft, G. G. Lunt: CEDIT: a C interface and macro facility for protein sequence alignment editing in colour with Microsoft Word 5.0 for PCs. 741-744
- C. D. Livingstone, Geoffrey J. Barton: Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. 745-756
- B. E. Nichols, Val C. Sheffield, Edwin M. Stone: A user-friendly Hypercard interface for human linkage analysis. 757-759
- A. Luttke, Rainer Fuchs: MacP12: a protein property multi-profile plot program for the Apple Macintosh. 760-761
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last updated on 2013-06-19T201401 by the dblp team