Journal: Bioinformatics

Volume 9, Issue 6

617 -- 627Alexander 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
629 -- 637V. 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
639 -- 645D. Bordo. ENVIRON: a software package to compare protein three-dimensional structures with homologous sequences using local structural motifs
647 -- 651Chiara Scapoli, A. Rodriguez-Larralde, S. Volinia, Italo Barrai. Enrichment of oligonucleotide sets with transcription control signals. III: DNA from non-mammalian vertebrates
653 -- 656W. H. Day, Fred R. McMorris. A consensus program for molecular sequences
657 -- 665M. Edwards, Roger E. Cooley. Expertise in expert systems: knowledge acquisition for biological expert systems
667 -- 670M. T. Semertzidis, S. Deplanque, J. P. Mornon. OMEGA: a three-dimensional databank for protein structures (a complement to PDB)
671 -- 680Edgardo A. Ferrán, Bernard Pflugfelder. A hybrid method to cluster protein sequences based on statistics and artificial neural networks
681 -- 685Salvatore Lanzavecchia, Pier Luigi Bellon, L. Tosoni. FT3D: three-dimensional Fourier analysis on small Unix workstations for electron microscopy and tomographic studies
687 -- 693F. Giuliano, P. Arrigo, F. Scalia, P. P. Cardo, G. Damiani. Potentially functional regions of nucleic acids recognized by a Kohonen s self-organizing map
695 -- 700Federico M. Stefanini, A. Camussi. APLOGEN: an object-oriented genetic algorithm performing Monte Carlo optimization
701 -- 707Sabino 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
709 -- 722C. M. Henneke. Protein motif by computer: the perfect Greek key jellyroll designer
723 -- 728S. J. Taylor, R. A. Rastall, J. T. Sykes, S. C. Winter, C. Bucke. Primary sequence analysis and representation techniques in carbohydrates
729 -- 734Geoffrey J. Barton. An efficient algorithm to locate all locally optimal alignments between two sequences allowing for gaps
735 -- 740Peter De Rijk, Rupert De Wachter. DCSE, an interactive tool for sequence alignment and secondary structure research
741 -- 744M. 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
745 -- 756C. D. Livingstone, Geoffrey J. Barton. Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation
757 -- 759B. E. Nichols, Val C. Sheffield, Edwin M. Stone. A user-friendly Hypercard interface for human linkage analysis
760 -- 761A. Luttke, Rainer Fuchs. MacP12: a protein property multi-profile plot program for the Apple Macintosh

Volume 9, Issue 5

491 -- 497A. 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
499 -- 509Michael Q. Zhang, T. G. Marr. A weight array method for splicing signal analysis
511 -- 515M. A. Shifman. PFGE MAPPER: a tool to aid in the analysis of pulse field gel electrophoresis maps
517 -- 522D. Yee, M. G. Prior, L. Z. Florence. Development of predictive models of laboratory animal growth using artificial neural networks
523 -- 529András Aszódi, William R. Taylor. Connection topology of proteins
531 -- 534K. C. Yan, F. T. Chau. SCANGRAPH: a program for digitization of graphs using an image scanner
535 -- 540A. Taberner, P. Castanera, E. Silvestre, Joaquín Dopazo. Estimation of the intrinsic rate of natural increase and its error by both algebraic and resampling approaches
541 -- 545N. Prunella, Sabino Liuni, Marcella Attimonelli, Graziano Pesole. FASTPAT: a fast and efficient algorithm for string searching in DNA sequences
547 -- 550G. Landini, J. W. Rippin. Notes on the implementation of the mass-radius method of fractal dimension estimation
551 -- 561G. Muller, C. Gaspin, A. Etienne, E. Westhof. Automatic display of RNA secondary structures
563 -- 571Pedro Mendes. GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems
573 -- 580Hermann-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
581 -- 586B. K. Kiong, Tin Wee Tan. A general UNIX interface for biocomputing and network information retrieval software
587 -- 591Rainer Fuchs. Block searches on VAX and Alpha computer systems
593 -- 596D. K. Green. Driving multiple pulsed field electrophoresis devices from one personal computer
597 -- 605P. L. Partner, M. L. Smith, W. Spoor, M. I. Clarkson. Computer simulation of selection in a hypothetical crop species
607 -- 610X. Salas, J. Portugal. PERFILS: a program for the quantitative treatment of footprinting data

Volume 9, Issue 4

381 -- 385R. Heilig, M. Hausmann, W. Rens, J. A. Aten, C. Cremer. Time-optimized analysis of slit-scan chromosome profiles on a general- purpose personal computer
387 -- 396Kun-Mao Chao, Ross C. Hardison, Webb Miller. Locating well-conserved regions within a pairwise alignment
397 -- 402Shashank Date, Rajendra Kulkarni, Bhavna Kulkarni, Urmila Kulkarni-Kale, Ashok S. Kolaskar. Multiple alignment of sequences on parallel computers
403 -- 405P. R. Hunter. A numerical method for allocating microbial isolates to strain types when characterized by typing methods that are not 100 reproducible
407 -- 411Aleksandar Milosavljevic, Jerzy Jurka. Discovering simple DNA sequences by the algorithmic significance method
413 -- 419A. Howard. SCUM - simulation of cyanobacterial underwater movement
421 -- 426David B. Searls. Doing sequence analysis with your printer
427 -- 434Norihiro Sakamoto, Toshihisa Takagi, Yasubumi Sakaki. Development of the Overlapping Oligonucleotide Database and its application to signal sequence search of the human genome
435 -- 440E. S. Shpigelman, Edward N. Trifonov, Alexander Bolshoy. CURVATURE: software for the analysis of curved DNA
441 -- 450H. M. Sauro. SCAMP: a general-purpose simulator and metabolic control analysis program
451 -- 458Alain Trubuil. Analysis of one-dimensional electrophoregrams
459 -- 464Hiroshi Dohi, Mitsuru Ishizuka, Shinsei Minoshima, Nobuyoshi Shimizu. GeneView: multi-language human gene mapping library with a graphical user interface
465 -- 467J. W. Brown. A toolkit for creating three-dimensional RNA pencil models
469 -- 471J. H. Nash. A computer program to calculate and design oligonucleotide primers from amino acid sequences
472 -- 0Z. Nesovic, George Harauz. 3DVISION: a program for display of three-dimensional wire models on a PC with VGA display
473 -- 0J. W. Brown. A Macintosh Hypercard compilation of small subunit ribosomal RNA sequences
475 -- 476W. X. Huang, M. I. Cohen, W. R. See. A fast graphics printing program for neurophysiological data
477 -- 478A. 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
479 -- 480J. M. Smith. OLIGOGET - a computerized database system for controlling oligonucleotide production

Volume 9, Issue 3

243 -- 251T. 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
253 -- 258N. N. Kozlov, E. I. Kugushev. Computer simulation of tRNA secondary structure folding
259 -- 265Kenji Satou, Emiko Furuichi, Kyoko Takiguchi, Toshihisa Takagi, Satoru Kuhara. A deductive database system PACADE for analyzing 3-D and secondary structures of protein
267 -- 273Masato Ishikawa, Tomoyuki Toya, Masaki Hoshida, Katsumi Nitta, A. Ogiwara, Minoru Kanehisa. Multiple sequence alignment by parallel simulated annealing
275 -- 283Jürgen Kleffe, E. Grau. The joint distribution of patterns in random sequences with application to the RC-measure for expressivity
285 -- 290V. V. Panjukov. Finding steady alignments: similarity and distance
291 -- 297A. Z. Maksyutov, E. S. Zagrebelnaya. ADEPT: a computer program for prediction of protein antigenic determinants
315 -- 324T. Rouxel, Antoine Danchin, Alain Hénaut. METALGEN.DB: metabolism linked to the genome of Escherichia coli, a graphics-oriented database
325 -- 330A. 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
331 -- 335D. N. Nedde, Matthew O. Ward. Visualizing relationships between nucleic acid sequences using correlation images
337 -- 342D. W. Collins. FISH: a guide to protein-coding DNA sequences in the GenBank database
343 -- 348Christophe Lefèvre, Joh-E Ikeda. The position end-set tree: a small automaton for word recognition in biological sequences
349 -- 354Christophe Lefèvre, Joh-E Ikeda. Pattern recognition in DNA sequences and its application to consensus foot-printing
355 -- 360J. Mrazek, J. Kypr. UNIREP: a microcomputer program to find unique and repetitive nucleotide sequences in genomes
361 -- 370Osamu Gotoh. Optimal alignment between groups of sequences and its application to multiple sequence alignment
371 -- 372Hedvig Hegyi, Sándor Pongor. Predicting potential domain homologies from FASTA search results
373 -- 374Scott R. Presnell, Bruce I. Cohen, Fred E. Cohen. MacMatch: a tool for pattern-based protein secondary structure prediction
375 -- 0Edward S. Chen, C. Asano, Daniel B. Davison. Parallel alignment of DNA sequences on the Connection Machine CM-2

Volume 9, Issue 2

123 -- 125Joaquín Dopazo, A. Rodriguez, J. C. Saiz, F. Sobrino. Design of primers for PCR amplification of highly variable genomes
133 -- 139J. E. Solomon, M. G. Harrington. A robust, high-sensitivity algorithm for automated detection of proteins in two-dimensional electrophoresis gels
141 -- 146Kiyoshi Asai, Satoru Hayamizu, Ken ichi Handa. Prediction of protein secondary structure by the hidden Markov model
147 -- 152F. Sasagawa, K. Tajima. Prediction of protein secondary structures by a neural network
153 -- 159Y. Matsuo, Minoru Kanehisa. An approach to systematic detection of protein structural motifs
161 -- 167Makoto Hirosawa, Masaki Hoshida, Masato Ishikawa, Tomoyuki Toya. MASCOT: multiple alignment system for protein sequences based on three- way dynamic programming
169 -- 176Webb Miller. Building multiple alignments from pairwise alignments
177 -- 182Yves Van de Peer, Rupert De Wachter. TREECON: a software package for the construction and drawing of evolutionary trees
183 -- 189K. Rohde, Peer Bork. A fast, sensitive pattern-matching approach for protein sequences
191 -- 196Claudine Landes, Alain Hénaut, Jean-Loup Risler. Dot-plot comparisons by multivariate analysis (DOCMA): a tool for classifying protein sequences
197 -- 199Gilbert Deléage, Christophe Geourjon. An interactive graphic program for calculating the secondary structure content of proteins from circular dichroism spectrum
201 -- 203A. 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
205 -- 209Pasquale Petrilli. Classification of protein sequences by their dipeptide composition
211 -- 214B. K. Kiong, Tin Wee Tan. A hypertext-like approach to navigating through the GCG sequence analysis package
215 -- 219A. Jamie Cuticchia, Jonathan Arnold, William E. Timberlake. ODS: ordering DNA sequences - a physical mapping algorithm based on simulated annealing
221 -- 226Barry S. Fagin, J. Gill Watt, R. Gross. A special-purpose processor for gene sequence analysis

Volume 9, Issue 1

1 -- 7Chut N. Yee, Lloyd Allison. Reconstruction of strings past
9 -- 15M. Suyama, A. Ogiwara, Takaaki Nishioka, J. Oda. Searching for amino acid sequence motifs among enzymes: the Enzyme- Reaction Database
17 -- 24Victor 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
25 -- 28G. Vogt, P. Argos. Profile sequence analysis and database searches on a transputer machine connected to a Macintosh computer
29 -- 35D. Krishna, P. J. Reddy. Microcomputer BASIC programs for rapid determination of lethal dosages of biocides using logit transformations
37 -- 44L. 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
45 -- 47M. Hauer-Jensen. Sample size calculation, power analysis and randomization: research project design in Windows
49 -- 57Thure Etzold, P. Argos. SRS - an indexing and retrieval tool for flat file data libraries
59 -- 64Thure Etzold, P. Argos. Transforming a set of biological flat file libraries to a fast access network
65 -- 69D. Venezia, P. J. O Hara. Rapid motif compliance scoring with match weight sets
71 -- 77Rainer Fuchs, Peter Stoehr. EMBL-search: a CD-ROM based database query system
79 -- 85R. 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
87 -- 91Christophe Geourjon, Gilbert Deléage. Interactive and graphic coupling between multiple alignments, secondary structure predictions and motif/pattern scanning into proteins
93 -- 100Valerio Balzarotti, V. Colizzi, S. Morante, Valerio Parisi. An algorithm for the identification of similar oligopeptides between amino acid sequences
101 -- 107Joaquín Dopazo, A. Taberner, A. Moya. Quantitative characterization of antigens using monoclonal antibody reactivities
109 -- 111G. H. Dibdin. Short algorithm to compensate for sampling-volume errors in diffusion- cell studies
113 -- 115D. S. Prestridge, Gary D. Stormo. SIGNAL SCAN 3.0: new database and program features
117 -- 118E. Wallin, C. Wettergren, F. Hedman, Gunnar von Heijne. Fast Needleman-Wunsch scanning of sequence databanks on a massively parallel computer