Journal: Bioinformatics

Volume 12, Issue 6

447 -- 454Jens Hanke, Jens G. Reich. Kohonen map as a visualization tool for the analysis of protein sequences: multiple alignments, domains and segments of secondary structures
455 -- 462F. Hospital, C. Dillmann, A. E. Melchinger. A general algorithm to compute multilocus genotype frequencies under various mating systems
463 -- 467Gilles Labesse. MulBlast 1.0: a multiple alignment of BLAST output to boost protein sequence similarity analysis
469 -- 471Andrew Rambaut, N. C. Grassly, S. Nee, P. H. Harvey. Bi-De: an application for simulating phylogenetic processes
473 -- 479Richard Hughey. Parallel hardware for sequence comparison and alignment
481 -- 489J. Wallman, Guy A. Hoelzer, D. J. Melnick. The effects of social structure, geographical structure, and population size on the evolution of mitochondrial DNA: I. A simulation model
491 -- 495U. S. Murty, K. Jamil, D. Krishna, P. J. Reddy. Rule-based system for the fast identification of species of Indian Anopheline mosquitoes
497 -- 506X. Huang, J. Zhang. Methods for comparing a DNA sequence with a protein sequence
507 -- 510Laurent Duret, Elisabeth Gasteiger, Guy Perrière. LALNVIEW: a graphical viewer for pairwise sequence alignments
511 -- 517Ying Xu, Edward C. Uberbacher. A polynomial-time algorithm for a class of protein threading problems
519 -- 524Guy Perrière, J. R. Lobry, Jean Thioulouse. Correspondence discriminant analysis: a multivariate method for comparing classes of protein and nucleic acid sequences
525 -- 529R. W. Hooft, Chris Sander, Michael Scharf, Gert Vriend. The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value
531 -- 537Salvatore Lanzavecchia, L. Tosoni, Pier Luigi Bellon. Fast sinogram computation and the sinogram-based alignment of images
543 -- 548Nicolas Galtier, Manolo Gouy, Christian Gautier. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny
549 -- 552L. Tosoni, Salvatore Lanzavecchia, Pier Luigi Bellon. Image and volume data rotation with 1- and 3-pass algorithms

Volume 12, Issue 5

361 -- 362Philipp Bucher, James W. Fickett, Artemis G. Hatzigeorgiou. Computational analysis of transcriptional regulatory elements: a field in flux
363 -- 374C. Fondrat, A. Kalogeropoulos. Approaching the function of new genes by detection of their potential upstream activation sequences in Saccharomyces cerevisiae: application to chromosome III
375 -- 381Craig J. Benham. Computation of DNA structural variability - a new predictor of DNA regulatory regions
383 -- 389Alexander Bolshoy, I. Ioshikhes, Edward N. Trifonov. Applicability of the multiple alignment algorithm for detection of weak patterns: periodically distributed DNA pattern as a study case
391 -- 398Gordon B. Hutchinson. The prediction of vertebrate promoter regions using differential hexamer frequency analysis
399 -- 404Luciano Milanesi, M. Muselli, P. Arrigo. Hamming-Clustering method for signals prediction in 5 and 3 regions of eukaryotic genes
405 -- 413Kerstin Quandt, Korbinian Grote, Thomas Werner. GenomeInspector: a new approach to detect correlation patterns of elements on genomic sequences
415 -- 422David A. Rosenblueth, Denis Thieffry, Araceli M. Huerta, Heladia Salgado, Julio Collado-Vides. Syntactic recognition of regulatory regions in Escherichia coli
423 -- 429Edward N. Trifonov. Interfering contexts of regulatory sequence elements
431 -- 439Jean-Michel Claverie, Stéphane Audic. The statistical significance of nucleotide position-weight matrix matches
441 -- 446Holger Karas, R. Knüppel, W. Schulz, Heinz Sklenar, Edgar Wingender. Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements

Volume 12, Issue 4

259 -- 267Jin Kim, James R. Cole, Sakti Pramanik. Alignment of possible secondary structures in multiple RNA sequences using simulated annealing
269 -- 280Suchendra M. Bhandarkar, Sridhar Chirravuri, Jonathan Arnold. PARODS - a study of parallel algorithms for ordering DNA sequences
281 -- 289Klaus Lindauer, Cezar Bendic, Jürgen Sühnel. HBexplore - a new tool for identifying and analysing hydrogen bonding patterns in biological macromolecules
291 -- 295Ingrid B. Jakobsen, Simon Easteal. A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences
297 -- 301I. Kuznetsov, P. Morozov. GEOMETRY: a software package for nucleotide sequence analysis using statistical geometry in sequence space
303 -- 310William Noble Grundy, Timothy L. Bailey, Charles Elkan. ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool
311 -- 318L. Hu, E. F. Saulinskas, P. Johnson, P. B. Harrington. Development of an expert system for amino acid sequence identification
319 -- 326Cheng-Che Chen, Richard O. Chen, Russ B. Altman. Constraining volume by matching the moments of a distance distribution
327 -- 345Kimmen Sjölander, Kevin Karplus, Michael Brown, Richard Hughey, Anders Krogh, I. Saira Mian, David Haussler. Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology
347 -- 351Joël-Paul Grillasca, Denis Aubert, Richard Planells, N. Domingo, H. Lafont. LITTLE KEVIN: a program for the estimation of protein homology by analysing the amino acid compositions and sequences
357 -- 358Roderic D. M. Page. TreeView: an application to display phylogenetic trees on personal computers

Volume 12, Issue 3

161 -- 170Igor B. Rogozin, Luciano Milanesi, Nikolay A. Kolchanov. Gene structure prediction using information on homologous protein sequence
171 -- 180Bruce A. Shapiro, Jin Chu Wu. An annealing mutation operator in the genetic algorithms for RNA folding
181 -- 183A. S. Law, D. W. Burt. qValue - a program to calculate comparative measures of genomic reorganisation from cytogenetic and/or linkage information
185 -- 189John A. Byers. TAXOKEY: a universal taxonomic key program using DOS text files and graphics
191 -- 196Raj K. Singh, D. L. Hoffman, Stephen G. Tell, C. Thomas White. BioSCAN: a network sharable computational resource for searching biosequence databases
197 -- 203Grit Herrmann, A. Schon, R. Brack-Werner, Thomas Werner. CONRAD: a method for identification of variable and conserved regions within proteins by scale-space filtering
205 -- 211A. Nakaya, Kenjiro Taura, K. Yamamoto, Akinori Yonezawa. Visualization of RNA secondary structures using highly parallel computers
213 -- 225Shigehiko Kanaya, Y. Kudo, Yasukazu Nakamura, Toshimichi Ikemura. Detection of genes in Escherichia coli sequences determined by genome projects and prediction of protein production levels, based on multivariate diversity in codon usage
227 -- 229Jürgen Sühnel. Image library of biological macromolecules
231 -- 235Y. Wada, H. Yasue. Development of an animal genome database and its search system
237 -- 240Kirill Degtyarenko, Péter Fábián. The directory of P450-containing systems on WorldWide Web
241 -- 245Jean-Paul Rolland, M. J. Flifla, Mireille Garreau, D. Thomas. IBIS version 3: an OSF/Motif-based interface for IBIS - integrated biological imaging system
247 -- 249O. Matzura, A. Wennborg. RNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows
251 -- 252Ross D. King, C. G. Angus. PM - protein music
253 -- 255V. Proutski, E. Holmes. Primer Master: a new program for the design and analysis of PCR primers
257 -- 258B. I. Osborne. Three sets of Macintosh AppleScripts for the automatic submission of sequence data to the internet BLAST server

Volume 12, Issue 2

4 -- 0G. Schaftenaar, K. Cuelenaere, Jan H. Noordik, Thure Etzold. A Tcl-based SRS v
81 -- 88Carlo Caporale, Ciro Sepe, Carla Caruso, Anna M. Garzillo, Vincenzo Buonocore. An algorithm to analyse the hydrolysis pathway of peptides and proteins by sequence analyses of unfractionated digestion mixtures
89 -- 94D. N. Perkins, Terri K. Attwood. XFINGER: a tool for searching and visualising protein fingerprints and patterns
95 -- 107Richard Hughey, Anders Krogh. Hidden Markov models for sequence analysis: extension and analysis of the basic method
109 -- 118Cathy H. Wu, S. Zhao, H.-L. Chen, C. J. Lo, Jerry McLarty. Motif identification neural design for rapid and sensitive protein family search
119 -- 127W. Vahrson, Klaus Hermann, Jürgen Kleffe, Burghardt Wittig. Object-oriented sequence analysis: SCL - a C++ class library
129 -- 133F. Eggenberger, Nicole Redaschi, Reinhard Doelz. FastAlert - an automatic search system to alert about new entries in biological sequence databanks
135 -- 143Jorja G. Henikoff, Steven Henikoff. Using substitution probabilities to improve position-specific scoring matrices
145 -- 150D. Curtis Jamison, Brad Mills, Bruce R. Schatz. An extensible network query unification system for biological databases
157 -- 160D. S. Prestridge. SIGNAL SCAN 4.0: additional databases and sequence formats

Volume 12, Issue 1

1 -- 8Giorgio Grillo, Marcella Attimonelli, Sabino Liuni, Graziano Pesole. CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases
9 -- 18Malcolm F. Wilkins, Lynne Boddy, Colin W. Morris, Richard Jonker. A comparison of some neural and non-neural methods for identification of phytoplankton from flow cytometry data
19 -- 24Sridhar Hannenhalli, W. Feldman, H. F. Lewis, Steven Skiena, Pavel A. Pevzner. Positional sequencing by hybridization
25 -- 30E. S. Carter II, C. S. Tung. NAMOT2 - a redesigned nucleic acid modeling tool: construction of non-canonical DNA structures
31 -- 40Xiaojun Guan, Edward C. Uberbacher. Alignments of DNA and protein sequences containing frameshift errors
41 -- 48Piero Fariselli, Rita Casadio. HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins
49 -- 54Vsevolod Makeev, Vladimir G. Tumanyan. Search of periodicities in primary structure of biopolymers: a general Fourier approach
63 -- 69Guy Perrière, Jean Thioulouse. On-line tools for sequence retrieval and multivariate statistics in molecular biology
71 -- 80F. Wolfertstetter, Kornelie Frech, Grit Herrmann, Thomas Werner. Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm