Journal: Bioinformatics

Volume 13, Issue 6

565 -- 581Ching Zhang, Andrew K. C. Wong. A genetic algorithm for multiple molecular sequence alignment
583 -- 586Jan Gorodkin, Laurie J. Heyer, Søren Brunak, Gary D. Stormo. Displaying the information contents of structural RNA alignments: the structure logos
593 -- 600H. Kato, Y. Takahashi. SS3D-P2: a three dimensional substructure search program for protein motifs based on secondary structure elements
601 -- 608Jérôme Gouzy, P. Eugene, Elizabeth A. Greene, Daniel Kahn, Florence Corpet. XDOM, a graphical tool to analyse domain arrangements in any set of protein sequences
609 -- 615Pascale Guerdoux-Jamet, Dominique Lavenier. SAMBA: hardware accelerator for biological sequence comparison
617 -- 618D. Fenyo. A software tool for the analysis of mass spectrometric disulfide mapping experiments
619 -- 620Hedvig Hegyi, J. M. Lai, Peer Bork. The Sequence Alerting Server - a new WEB server
621 -- 622T. Sicheritz-Ponten. BioWish: a molecular biology command extension to Tcl/Tk
623 -- 624A. S. Law, D. W. Burt. Two applications to facilitate the viewing of database search result files on the Macintosh
625 -- 626Jens Stoye, Vincent Moulton, Andreas W. M. Dress. DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment

Volume 13, Issue 5

487 -- 496Ilya N. Shindyalov, Philip E. Bourne. Protein data representation and query using optimized data decomposition
497 -- 508S. Goldberg, P. Ferrand, N. Q. Nguyen, Jean-François Boisvieux, Serge A. Hazout. Bi-dimensional scaling map (BDS-Map): an approach for building large genetic maps
509 -- 522Inge Jonassen. Efficient discovery of conserved patterns using a pattern graph
523 -- 535Carol Soderlund, I. Longden, Richard Mott. FPC: a system for building contigs from restriction fingerprinted clones
537 -- 543Ronald G. Forsythe Jr., Peter D. Karp, Michael L. Mavrovouniotis. Estimation of equilibrium constants using automated group contribution methods
545 -- 547Benny Shomer. Seqalert - a daily sequence alertness server for the EMBL and SWISSPROT databases
549 -- 554Hugh E. Williams, Justin Zobel. Compression of nucleotide databases for fast searching
555 -- 556Z. Yang. PAML: a program package for phylogenetic analysis by maximum likelihood
557 -- 558W. Gronwald, Robert F. Boyko, Brian D. Sykes. GSC: a graphical program for NMR chemical shift comparison
559 -- 560N. C. Grassly, J. Adachi, Andrew Rambaut. PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees
561 -- 562David S. Wishart, S. Fortin, David R. Woloschuk, W. Wong, T. Rosborough, Gary H. Van Domselaar, Jonathan Schaeffer, Duane Szafron. A platform-independent graphical user interface for SEQSEE and XALIGN
563 -- 564Jean-Paul Rolland, P. Bon, D. Thomas. MACS: automatic counting of objects based on shape recognition

Volume 13, Issue 4

325 -- 332William R. Pearson. Identifying distantly related protein sequences
333 -- 344David B. Searls. Linguistic approaches to biological sequences
345 -- 356Burkhard Rost, Seán I. O Donoghue. Sisyphus and prediction of protein structure
357 -- 364Tatsuya Akutsu, Kentaro Onizuka, Masato Ishikawa. Rapid protein fragment search using hash functions based on the Fourier transform
365 -- 376Steven Salzberg. A method for identifying splice sites and translational start sites in eukaryotic mRNA
377 -- 385J. H. Hofmeyr, A. Cornish-Bowden. The reversible Hill equation: how to incorporate cooperative enzymes into metabolic models
387 -- 396Hiroyuki Toh. Introduction of a distance cut-off into structural alignment by the double dynamic programming algorithm
397 -- 406William Noble Grundy, Timothy L. Bailey, Charles Elkan, Michael E. Baker. Meta-MEME: motif-based hidden Markov models of protein families
407 -- 413P. Durand, L. Canard, J. P. Mornon. Visual BLAST and visual FASTA: graphic workbenches for interactive analysis of full BLAST and FASTA outputs under Microsoft Windows 95/NT
415 -- 424M. Ito, Y. Matsuo, Ken Nishikawa. Prediction of protein secondary structure using the 3D-1D compatibility algorithm
425 -- 430R. W. Hooft, Chris Sander, Gert Vriend. Objectively judging the quality of a protein structure from a Ramachandran plot
431 -- 438V. Biaudet, Franck Samson, Philippe Bessières. Micado - a network-oriented database for microbial genomes
439 -- 444S. Lay, D. Bray. A computer program for the analysis of protein complex formation
445 -- 451J. Schafer, M. Schoniger. DISTREE: a tool for estimating genetic distances between aligned DNA sequences
453 -- 457R. W. Gill, T. Charles Hodgman, C. B. Littler, M. D. Oxer, D. S. Montgomery, S. Taylor, P. Sanseau. A new dynamic tool to perform assembly of expressed sequence tags (ESTs)
459 -- 471Bruce A. Shapiro, Jin Chu Wu. Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm
473 -- 474Ross D. King, Mansoor A. S. Saqi, Roger A. Sayle, Michael J. E. Sternberg. DSC: public domain protein secondary structure predication
475 -- 476L. I. Toldo. JaMBW 1.1: Java-based Molecular Biologists Workbench
477 -- 478Richard Mott. EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA
481 -- 483Miguel A. Andrade, Georg Casari, Antoine de Daruvar, Chris Sander, Reinhard Schneider, Javier Tamames, Alfonso Valencia, Christos A. Ouzounis. Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function
485 -- 486E. Lorenz, S. Leeton, R. J. Owen. A simple method for sizing large fragments of bacterial DNA separated by PFGE

Volume 13, Issue 3

211 -- 215R. R. Mallios. An iterative algorithm for converting a class II MHC binding motif into a quantitative predictive model
217 -- 225Prakash M. Nadkarni. Mapdiff: determining differences between two genomic maps
227 -- 230Yves Van de Peer, Rupert De Wachter. Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites
231 -- 234Patrick Aloy, Juan Cedano, Baldomero Oliva, Francesc X. Avilés, Enrique Querol. TransMem : a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins
235 -- 238Andrew Rambaut, N. C. Grassly. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
239 -- 241Rainer Fuchs. Grouper - creation of marker sets for multiplexed genotyping
243 -- 248Anatoly S. Frolov, I. S. Pika, A. M. Eroshkin. ProMSED: protein multiple sequence editor for Windows 3.11/95
249 -- 256Eric Depiereux, G. Baudoux, P. Briffeuil, I. Reginster, Xavier De Bolle, C. Vinals, Ernest Feytmans. Match-Box_server: a multiple sequence alignment tool placing emphasis on reliability
257 -- 262Josef Pánek, Jiri Vohradsky. Object-oriented developmental environment for image-analysis applications: implementation for 2D gel electrophoretogram analysis
263 -- 270S. Tiwari, S. Ramachandran, A. Bhattacharya, S. Bhattacharya, R. Ramaswamy. Prediction of probable genes by Fourier analysis of genomic sequences
271 -- 279L. Ehrlich, C. Munkel, G. Chirico, J. Langowski. A Brownian dynamics model for the chromatin fiber
281 -- 290S. Panzer, L. Cooley, Perry L. Miller. Using explicitly represented biological relationships for database navigation and searching via the World-Wide Web
291 -- 295Gilles Labesse, N. Colloc h, Joël Pothier, J. P. Mornon. P-SEA: a new efficient assignment of secondary structure from C alpha trace of proteins
297 -- 301András Fiser, Zsuzsanna Dosztányi, István Simon. The role of long-range interactions in defining the secondary structure of proteins is overestimated
303 -- 306Andrew Rambaut, P. H. Harvey, S. Nee. End-Epi: an application for inferring phylogenetic and population dynamical processes from molecular sequences
307 -- 311Julio Rozas, Ricardo Rozas. DnaSP version 2.0: a novel software package for extensive molecular population genetics analysis
313 -- 317Joaquín Dopazo. A new index to find regions showing an unexpected variability or conservation in sequence alignments
319 -- 321Florencio Pazos, O. Olmea, Alfonso Valencia. A graphical interface for correlated mutations and other protein structure prediction methods
323 -- 324Y. Wada, K. Inoue, K. Ohga, H. Yasue. Software tool for gene mapping: gRanch

Volume 13, Issue 2

115 -- 122Alexander G. Bachinsky, Andrey A. Yarigin, E. H. Guseva, V. A. Kulichkov, Lily Ph. Nizolenko. A bank of protein family patterns for rapid identification of possible functions of amino acid sequences
123 -- 130J. H. Woods, H. M. Sauro. Elasticities in Metabolic Control Analysis: algebraic derivation of simplified expressions
131 -- 136Eric Rivals, Olivier Delgrange, Jean-Paul Delahaye, Max Dauchet, Marie-Odile Delorme, Alain Hénaut, Emmanuelle Ollivier. Detection of significant patterns by compression algorithms: the case of approximate tandem repeats in DNA sequences
137 -- 143Eric Glémet, Jean-Jacques Codani. LASSAP, a LArge Scale Sequence compArison Package
145 -- 150A. Wozniak. Using video-oriented instructions to speed up sequence comparison
151 -- 158Jacek Blazewicz, Janusz Kaczmarek, Marta Kasprzak, Wojciech T. Markiewicz, Jan Weglarz. Sequential and parallel algorithms for DNA sequencing
159 -- 167R. Varón, F. García Sevilla, M. García-Moreno, F. García-Cánovas, R. Peyro, R. G. Duggleby. Computer program for the equations describing the steady state of enzyme reactions
169 -- 174L. Winder, M. Lefley, B. Smith. A key for freshwater invertebrates using fuzzy logic
175 -- 182Todd Smith, Chris Abajian, Leroy E. Hood. Hopper: software for automating data tracking and flow in DNA sequencing
183 -- 190Y. Tsukamoto, Kyoko Takiguchi, Kenji Satou, Emiko Furuichi, Toshihisa Takagi, Satoru Kuhara. Application of a deductive database system to search for topological and similar three-dimensional structures in protein
191 -- 199Christian Barrett, Richard Hughey, Kevin Karplus. Scoring hidden Markov models
205 -- 210I. Belyi, Pavel A. Pevzner. Software for DNA sequencing by hybridization

Volume 13, Issue 1

1 -- 12Kathleen M. Currey, Bruce A. Shapiro. Secondary structure computer prediction of the poliovirus 5 non-coding region is improved by a genetic algorithm
13 -- 22G. Chelvanayagam, Simon Easteal. Correlating patterns in alignments of polymorphic sequences with experimental assays
23 -- 28Asaf A. Salamov, Victor V. Solovyev. Recognition of 3 -processing sites of human mRNA precursors
29 -- 35Q. K. Chen, G. Z. Hertz, Gary D. Stormo. PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices
37 -- 44E. V. Korotkov, M. A. Korotkova, J. S. Tulko. Latent sequence periodicity of some oncogenes and DNA-binding protein genes
45 -- 53J. Alicia Grice, Richard Hughey, Don Speck. Reduced space sequence alignment
55 -- 60Benny Shomer. EMBL sequence submission system--an object-oriented approach to developing interactive data collection systems through the WWW
69 -- 73C. Chevalet, Jérôme Gouzy, M. SanCristobal-Gaudy. Regional assignment of genetic markers using a somatic cell hybrid panel: a WWW interactive program available for the pig genome
75 -- 80Kun-Mao Chao, Jinghui Zhang, James Ostell, Webb Miller. A tool for aligning very similar DNA sequences
81 -- 87G. S. Miller, Rainer Fuchs. Post-processing of BLAST results using databases of clustered sequences
89 -- 97Kornelie Frech, Kerstin Quandt, Thomas Werner. Software for the analysis of DNA sequence elements of transcription
99 -- 106Michael G. Roberts, D. A. Phoenix, A. R. Pewsey. An algorithm for the detection of surface-active alpha helices with the potential to anchor proteins at the membrane interface
107 -- 108W. Bains. Hexanucleotide frequency database
109 -- 110Kornelie Frech, P. Dietze, Thomas Werner. ConsInspector 3.0: new library and enhanced functionality
111 -- 113Alexis S. Ivanov, Andrey B. Rumjantsev, Vladlen S. Skvortsov, Alexander I. Archakov. ONIX: an interactive PC program for the examination of protein 3D structure from PDB