Journal: Bioinformatics

Volume 8, Issue 6

529 -- 534Victor B. Strelets, Ilya N. Shindyalov, Nikolay A. Kolchanov, Luciano Milanesi. Fast, statistically based alignment of amino acid sequences on the base of diagonal fragments of DOT-matrices
539 -- 548D. Waddington, D. W. Burt. Estimation of restriction maps with known site order using a generalized linear model [published erratum appears in Comput Appl Biosci 1993 Apr;9(2): 242]
549 -- 554A. Alvarruiz, A. Gutierrez, M. Rodrigo. APL program for evaluation of heat processes for spherical foods
555 -- 562J. Lee. Cumulative logit modelling for ordinal response variables: applications to biomedical research
563 -- 567G. Bouffard, James Ostell, Kenneth E. Rudd. GeneScape: a relational database of Escherichia coli genomic map data for Macintosh computers
569 -- 574A. Guénoche. Can we recover a sequence, just knowing all its subsequences of given length?
575 -- 577F. Rodriguez, M. Prats. Time correction for computing Michaelis-Menten kinetics
579 -- 581C. M. Comiskey, H. J. Ruskin. AIDS in Ireland: the reporting delay distribution and the implementation of integral equation models
583 -- 586M. J. Flifla, Mireille Garreau, Jean-Paul Rolland, Jean-Louis Coatrieux, D. Thomas. IBIS integrated biological imaging system: electron micrograph image-processing software running on Unix workstations
591 -- 594A. Luttke, Rainer Fuchs. MacT: Apple Macintosh programs for constructing phylogenetic trees
595 -- 597R. Schipper, M. Kenter, T. Rinke de Wit, J. D'Amaro. A personal computer program for large-scale comparisons of related nucleotide sequences
599 -- 600J. Heringa, H. Sommerfeldt, Desmond G. Higgins, P. Argos. OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity
601 -- 602M. Dubnick. Btab - a Blast output parser
605 -- 0A. Howard. MIGS - a simple graphics utility program

Volume 8, Issue 5

425 -- 431Kira S. Makarova, A. V. Mazin, Yuri I. Wolf, V. V. Soloviev. DIROM: an experimental design interactive system for directed mutagenesis and nucleic acids engineering
433 -- 441Jürgen Kleffe, Mark Borodovsky. First and second moment of counts of words in random texts generated by Markov chains
443 -- 449H. J. Stoffers, Erik L. L. Sonnhammer, G. J. Blommestijn, N. J. Raat, H. V. Westerhoff. METASIM: object-oriented modelling of cell regulation
451 -- 459D. J. Parry-Smith, Terri K. Attwood. ADSP - a new package for computational sequence analysis
461 -- 466J. D. Parsons, S. Brenner, M. J. Bishop. Clustering cDNA sequences
467 -- 474A. Jamie Cuticchia, Jonathan Arnold, H. Brody, William E. Timberlake. CMAP: contig mapping and analysis package, a relational database for chromosome reconstruction
475 -- 479G. W. Dombi. Limitations of Augustinsson plots
481 -- 487Kun-Mao Chao, William R. Pearson, Webb Miller. Aligning two sequences within a specified diagonal band
489 -- 500G. H. Dibdin. A finite-difference computer model of solute diffusion in bacterial films with simultaneous metabolism and chemical reaction
501 -- 509Eric Depiereux, Ernest Feytmans. MATCH-BOX: a fundamentally new algorithm for the simultaneous alignment of several protein sequences
511 -- 520X. Huang, Michael S. Waterman. Dynamic programming algorithms for restriction map comparison
521 -- 523Denis C. Shields, Desmond G. Higgins, P. M. Sharp. GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content
524 -- 0J. Mrazek, A. Spanova. ANAGEL: a personal computer program for evaluating DNA fragment lengths from distances migrated in an agarose gel

Volume 8, Issue 4

307 -- 309P. Paz, J. Renau Piqueras, E. J. Tizado. A program for the application of the radial distribution function to cluster analysis in cell biology
311 -- 321Nabil Kamel. A profile for molecular biology databases and information resources
339 -- 345N. N. Alexandrov. Local multiple alignment by consensus matrix
347 -- 357Peter D. Karp. A knowledge base of the chemical compounds of intermediary metabolism
367 -- 376Mineichi Kudo, S. Kitamura-Abe, Masaru Shimbo, Y. Lida. Analysis of context of 5 -splice site sequences in mammalian mRNA precursors by subclass method
377 -- 383R. Jones. Sequence pattern matching on a massively parallel computer
385 -- 388J. A. Lopez-Bueno, A. Moya. GEOSEQ: a Pascal program to calculate statistical geometry parameters of aligned nucleic acid sequences
389 -- 399M. Schmitz, G. Steger. Base-pair probability profiles of RNA secondary structures
401 -- 404J. Mrazek, J. Kypr. DNABIND: an interactive microcomputer program searching for nucleotide sequences that may code for conserved DNA-binding protein motifs
405 -- 406J. Lee. Comparison of variance between correlated samples
407 -- 408R. L. Read, D. Davison, J. E. Chappelear, John S. Garavelli. GBPARSE: a parser for the GenBank flat-file format with the new feature table format
409 -- 0F. Dessaint. Chull.sas: an SAS macro to construct the convex hull of one (or more) finite sets of points in a plane

Volume 8, Issue 3

209 -- 213P. J. Reddy, D. Krishna, U. S. Murty, K. Jamil. A microcomputer FORTRAN program for rapid determination of lethal concentrations of biocides in mosquito control
215 -- 225C. Chevalet, B. Michot. An algorithm for comparing RNA secondary structures and searching for similar substructures
227 -- 238Dong-Guk Shin, Changhwan Lee, Jinghui Zhang, Kenneth E. Rudd, Claire M. Berg. Redesigning, implementing and integrating Escherichia coli genome software tools with an object-oriented database system
239 -- 241H. Pasternak, B. A. Shalev. An algorithm to fit the Gompertz function to growth curves
243 -- 248Jih-H. Chen, Shu-Yun Le, Jacob V. Maizel. A procedure for RNA pseudoknot prediction
249 -- 254J. C. Wallace, Steven Henikoff. PATMAT: a searching and extraction program for sequence, pattern and block queries and databases
255 -- 260Colombe Chappey, Serge A. Hazout. A method for delineating structurally homogeneous regions in protein sequences
261 -- 265A. Friemann, S. Schmitz. A new approach for displaying identities and differences among aligned amino acid sequences
275 -- 282David T. Jones, William R. Taylor, Janet M. Thornton. The rapid generation of mutation data matrices from protein sequences
283 -- 289B. Robson, P. J. Greaney. Natural sequence code representations for compression and rapid searching of human-genome style databases
291 -- 292M. Dubnick. STATUS, SEQSTAT, CSTATUS and LOAD: computer programs that facilitate large DNA-sequencing projects
293 -- 294O. Gefeller. A simple method of avoiding the computational problems of the delta method for the end-user of statistical packages
295 -- 296D. Akrigg, Terri K. Attwood, Alan J. Bleasby, John B. C. Findlay, A. C. North, N. A. Maughan, D. J. Parry-Smith, D. N. Perkins, J. C. Wootton. SERPENT - an information storage and analysis resource for protein sequences

Volume 8, Issue 2

97 -- 106Giles T. Innocent. An investigation of the epidemiology of neuroblastoma in children under the age of 15 years in England, Scotland and Wales
121 -- 127Pavel A. Pevzner. Statistical distance between texts and filtration methods in sequence comparison
129 -- 135Mikhail S. Gelfand, C. G. Kozhukhin, Pavel A. Pevzner. Extendable words in nucleotide sequences
137 -- 139Desmond G. Higgins, Peter Stoehr. EMBLSCAN: fast approximate DNA database searches on compact disc
141 -- 147Perry L. Miller, Prakash M. Nadkarni, P. A. Bercovitz. Harnessing networked workstations as a powerful parallel computer: a general paradigm illustrated using three programs for genetic linkage analysis
149 -- 154F. R. Rysavy, M. J. Bishop, G. P. Gibbs, G. W. Williams. The UK Human Genome Mapping Project online computing service
155 -- 165Xiaoqiu Huang, Webb Miller, Scott Schwartz, Ross C. Hardison. Parallelization of a local similarity algorithm
167 -- 175Perry L. Miller, Prakash M. Nadkarni, William R. Pearson. Comparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison
185 -- 188M. D. Partis. MOMENT: software for analysis and display of amphiphilic regions in proteins
189 -- 191Desmond G. Higgins, Alan J. Bleasby, Rainer Fuchs. CLUSTAL V: improved software for multiple sequence alignment
195 -- 0Gianluca De Bellis, I. R. Consani, M. Manoni, R. Pergolizzi, M. Luzzana. Fluorescent automated DNA sequencers: a file exchange program
196 -- 198John A. Byers. REF-LIST: program to list references found in DOS text files of scientific manuscripts
199 -- 0R. Jones. Alerting users to relevant new entries in the GenBank DNA sequence database

Volume 8, Issue 1

1 -- 4R. A. Sutherland, M. D. Partis. Using fragment lengths from incomplete digestion by multiply cleaving enzymes to map antibody binding sites on a protein
5 -- 14Didier Arquès, Christian J. Michel, K. Orieux. Analysis of gene evolution: the software AGE
15 -- 22Desmond G. Higgins. Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets
23 -- 27J. Lee, C. Yoshizawa, L. Wilkens, H. P. Lee. Covariance adjustment of survival curves based on Cox s proportional hazards regression model
29 -- 34J. Mrazek, J. Kypr. GLOBIC: a very fast microcomputer program for fingerprinting, characterization and comparison of long nucleotide sequences
35 -- 38Mauno Vihinen, A. Euranto, P. Luostarinen, Olli Nevalainen. MULTICOMP: a program package for multiple sequence comparison
39 -- 44Edgardo A. Ferrán, Pascual Ferrara. Clustering proteins into families using artificial neural networks [published erratum appears in Comput Appl Biosci 1992 Jun;8(3): 305]
45 -- 48Peter R. Sibbald, H. Sommerfeldt, P. Argos. Overseer: a nucleotide sequence searching tool
49 -- 55G. Vogt, P. Argos. Searching for distantly related protein sequences in large databases by parallel processing on a transputer machine
57 -- 64Mikhail A. Roytberg. A search for common patterns in many sequences
65 -- 70J. Nedelman, P. Heagerty, C. Lawrence. Quantitative PCR with internal controls
71 -- 73V. B. Cockcroft, J. T. Pedersen, G. G. Lunt, David J. Osguthorpe. BIOSITE: a program for the interactive comparison of aligned homologous protein sequences
75 -- 77Christiaan Karreman. A dotplot program for the Atari ST, for the analysis of DNA and protein sequences
79 -- 80V. E. Babenko, V. R. Sagitov. VECTOR-PC: a flexible tool for the design, display and retrieval of information regarding to cloning vectors
81 -- 0Marc Eberhard, Bernd Leister, Cornelia Stoppkotte. MULTI: a program for multicomponent analysis of spectra
83 -- 0B. I. Osborne. HyperPCR: a Macintosh Hypercard program for the determination of optimal PCR annealing temperature