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ORCIDComputer Applications in the Biosciences, Volume 9
Volume 9, Number 1, February 1993
- Chut N. Yee, Lloyd Allison:
Reconstruction of strings past. 1-7
- Mikita 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 - G. Vogt, P. Argos:
Profile sequence analysis and database searches on a transputer machine connected to a Macintosh computer. 25-28 - 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:
SRS - an indexing and retrieval tool for flat file data libraries. 49-57 - Thure Etzold, P. Argos:
Transforming a set of biological flat file libraries to a fast access network. 59-64 - D. Venezia, P. J. O'Hara:
Rapid motif compliance scoring with match weight sets. 65-69 - Rainer Fuchs, Peter Stoehr:
EMBL-search: a CD-ROM based database query system. 71-77 - Ronny 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, Ana Taberner, Andrés 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 - Dan S. Prestridge, Gary D. Stormo:
SIGNAL SCAN 3.0: new database and program features. 113-115 - Erik Wallin, Christian Wettergren, Fredrik 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, Francisco 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 - Jerry 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 - F. Sasagawa, K. Tajima:
Prediction of protein secondary structures by a neural network. 147-152 - Yo 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 - K. Rohde, Peer Bork:
A fast, sensitive pattern-matching approach for protein sequences. 183-189 - 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 P. 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 P. 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 - N. N. Kozlov, E. I. Kugushev:
Computer simulation of tRNA secondary structure folding. 253-258 - 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 - G. Mehldau, G. Myers:
A system for pattern matching applications on biosequences. 299-314 - 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, Alkis 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 - Jan Mrázek, J. Kypr:
UNIREP: a microcomputer program to find unique and repetitive nucleotide sequences in genomes. 355-360 - 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
- Rainer Heilig, Michael Hausmann, Willem Rens, Jacob A. Aten, Christoph 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 - Alan 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 - Herbert 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 - Judith 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 - Michael Q. Zhang, T. G. Marr:
A weight array method for splicing signal analysis. 499-509 - 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. Zack Florence:
Development of predictive models of laboratory animal growth using artificial neural networks. 517-522 - András Aszódi, William R. Taylor:
Connection topology of proteins. 523-529 - K. C. Yan, F. T. Chau:
SCANGRAPH: a program for digitization of graphs using an image scanner. 531-534 - Ana Taberner, Pedro Castanera, Enrique 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 - Gabriel Landini, John 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 - William H. E. Day, Fred R. McMorris:
A consensus program for molecular sequences. 653-656 - Marion 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 - Simon J. E. Taylor, R. A. Rastall, J. T. Sykes, Stephen 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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