Journal: Bioinformatics

Volume 10, Issue 6

575 -- 586Weider Chang, Ilya N. Shindyalov, Calton Pu, Philip E. Bourne. Design and application of PDBlib, a C++ macromolecular class library
587 -- 596Adam Godzik, Jeffrey Skolnick. Flexible algorithm for direct multiple alignment of protein structures and sequences
597 -- 603. Construction of a generalized consensus matrix for recognition of vertebrate pre-mRNA 3 -terminal processing sites
605 -- 611V. A. Shepelev, N. V. Yanishevsky. Multidimensional dot-matrices
613 -- 623Ying Xu, Richard J. Mural, Edward C. Uberbacher. Constructing gene models from accurately predicted exons: an application of dynamic programming
625 -- 634Yuhong Wang, Rolf A. Prade, James Griffith, William E. Timberlake, Jonathan Arnold. ODS_BOOTSTRAP: assessing the statistical reliability of physical maps by bootstrap resampling
635 -- 645Gisbert Schneider, Johannes Schuchhardt, Paul Wrede. Artificial neural networks and simulated molecular evolution are potential tools for sequence-oriented protein design
647 -- 655Pankaj Agarwal. Simulation of aggregation in Dictyostelium using the Cell Programming Language
657 -- 660T. N. Bryant. Identifying correct bacteriological vocabulary: software to look up RKC codes and statements
661 -- 669Victor V. Solovyev, Asaf A. Salamov. Predicting alpha-helix and beta-strand segments of globular proteins
671 -- 675Steven W. Smith, Ross A. Overbeek, Carl R. Woese, W. Gilbert, P. M. Gillevet. The genetic data environment an expandable GUI for multiple sequence analysis
677 -- 680M. L. Cain, L. W. Murray. Non-linear regression models to estimate the size of DNA fragments
681 -- 683S. R. Wilson, P. J. Solomon. Estimates for different stages of HIV/AIDS disease
685 -- 686M. G. Claros, Gunnar von Heijne. TopPred II: an improved software for membrane protein structure predictions
687 -- 688David S. Wishart, Robert F. Boyko, Brian D. Sykes. Constrained multiple sequence alignment using XALIGN

Volume 10, Issue 5

465 -- 470Chiara Scapoli, A. Rodriguez-Larralde, S. Volinia, M. Beretta, Italo Barrai. Identification of a set of frequent decanucleotides in plants and in animals
471 -- 476D. Bray, S. Lay. Rapid numerical integration algorithm for finding the equilibrium state of a system of coupled binding reactions
477 -- 488M. Farza, A. Cheruy. BIOESTIM: software for automatic design of estimators in bioprocess engineering
489 -- 494Carlo Caporale, Ciro Sepe, Carla Caruso, Pasquale Petrilli, Vincenzo Buonocore. An algorithm to determine protein sequence alignment by utilizing data obtained from a peptide mixture and individual peptides
495 -- 500J. Clotet, Juan Cedano, Enrique Querol. An Excel spreadsheet computer program combining algorithms for prediction of protein structural characteristics
501 -- 508R. Gambari, S. Volinia, Carlo Nesti, Chiara Scapoli, Italo Barrai. A set of Alu-free frequent decamers from mammalian genomes enriched in transcription factor signals
509 -- 511Oswaldo Trelles-Salazar, Emilio L. Zapata, José María Carazo. On an efficient parallelization of exhaustive sequence comparison algorithms on message passing architectures
513 -- 517Y. Elkind, B. Nir, J. I. Weller. Maximum likelihood estimation of quantitative trait loci parameters with the aid of genetic markers using a standard statistical package
519 -- 526Klaus Heumann, David G. George, Hans-Werner Mewes. A new concept of sequence data distribution on wide area networks
527 -- 535L. A. Parodi, C. A. Granatir, Gerald M. Maggiora. A consensus procedure for predicting the location of alpha-helical transmembrane segments in proteins
537 -- 544Janos Posfai, Z. Szaraz, Richard J. Roberts. VISA: Visual Sequence Analysis for the comparison of multiple amino acid sequences
545 -- 546Mansoor A. S. Saqi, Roger A. Sayle. PdbMotif--a tool for the automatic identification and display of motifs in protein structures
547 -- 550Kenta Nakai, T. Tokimori, A. Ogiwara, I. Uchiyama, T. Niiyama. Gnome - an Internet-based sequence analysis tool
551 -- 557L. L. Walsh. Navigating the Brookhaven Protein Data Bank
567 -- 568Michael L. Engle, Christian Burks. GenFrag 2.1: new features for more robust fragment assembly benchmarks
569 -- 570Yves Van de Peer, Rupert De Wachter. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment

Volume 10, Issue 4

369 -- 378K. W. Hart, David B. Searls, G. Christian Overton. SORTEZ: a relational translator for NCBI s ASN.1 database
379 -- 387Osamu Gotoh. Further improvement in methods of group-to-group sequence alignment with generalized profile operations
389 -- 399Florence Corpet, B. Michot. RNAlign program: alignment of RNA sequences using both primary and secondary structures
401 -- 408A. Gleizes, Alain Hénaut. A global approach for contig construction
409 -- 412Andrey Rzhetsky, Masatoshi Nei. METREE: a program package for inferring and testing minimum-evolution trees
413 -- 417Rainer Fuchs. Sequence analysis by electronic mail: a tool for accessing Internet e- mail servers
419 -- 426Jin Kim, Sakti Pramanik, M. J. Chung. Multiple sequence alignment using simulated annealing
427 -- 433C. S. Tung, E. S. Carter II. Nucleic acid modeling tool (NAMOT): an interactive graphic tool for modeling nucleic acid structures
435 -- 442L. W. Wright, J. B. Lichter, John Reinitz, M. A. Shifman, Kenneth K. Kidd, Perry L. Miller. Computer-assisted restriction mapping: an integrated approach to handling experimental uncertainty
443 -- 447A. Fire. A four-dimensional digital image archiving system for cell lineage tracing and retrospective embryology
453 -- 454Claudine Landes, Jean-Loup Risler. Fast databank searching with a reduced amino-acid alphabet
455 -- 456W. Miller, Mark Boguski. A note about computing all local alignments
457 -- 459Roman L. Tatusov, Eugene V. Koonin. A simple tool to search for sequence motifs that are conserved in BLAST outputs

Volume 10, Issue 3

219 -- 225X. Huang. An algorithm for identifying regions of a DNA sequence that satisfy a content requirement
227 -- 235X. Huang. On global sequence alignment
243 -- 247B. Golding. Exploratory analysis of multiple sequence alignments using phylogenies
249 -- 261J. A. Inglehart, P. C. Nelson. On the limitations of automated restriction mapping
263 -- 271Elias Zintzaras, N. P. Brown, A. Kowald. Growing a classification tree using the apparent misclassification rate
273 -- 275F. Dardel. MC-Fit: using Monte-Carlo methods to get accurate confidence limits on enzyme parameters
277 -- 280Fabio E. Penotti. A distributed system for DNA/protein database similarity searches
281 -- 284P. R. Reeves, L. Farnell, R. Lan. MULTICOMP: a program for preparing sequence data for phylogenetic analysis
285 -- 294Malcolm F. Wilkins, Colin W. Morris, Lynne Boddy. A comparison of Radial Basis Function and backpropagation neural networks for identification of marine phytoplankton from multivariate flow cytometry data
295 -- 299E. M. el-Mansi, G. C. Dawson, C. F. Bryce. Steady-state modelling of metabolic flux between the tricarboxylic acid cycle and the glyoxylate bypass in Escherichia coli
301 -- 307Erik L. L. Sonnhammer, Richard Durbin. A workbench for large-scale sequence homology analysis
309 -- 317P. Zhang, E. A. Schon, S. G. Fischer, E. Cayanis, J. Weiss, S. Kistler, Philip E. Bourne. An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA
319 -- 322Victor B. Strelets, Andrey A. Ptitsyn, Luciano Milanesi, Hwa A. Lim. Data bank homology search algorithm with linear computation complexity
329 -- 334T. N. Bryant. A bacterial identification teaching exercise revisited
335 -- 339S. A. Sammons, D. P. Dykes. OLGCG: an OPEN LOOK interface to the GCG sequence analysis package
341 -- 348L. B. Ellis, R. P. Milius. Valid and invalid implementations of GOR secondary structure predictions
349 -- 358Carol Soderlund, Christian Burks. GRAM and genfragII: solving and testing the single-digest, partially ordered restriction map problem
359 -- 360T. N. Bryant. A program for reordering coded data
361 -- 362Prakash M. Nadkarni, S. T. Reeders, J. Zhou. A modification of the ALIGN program to assist visual interpretation of mutated sequences

Volume 10, Issue 2

85 -- 103M. Levin. A Julia set model of field-directed morphogenesis: developmental biology and artificial life
105 -- 109L. Rosenthaler, Reinhard Doelz. Simplified user poll and experience report language (SUPER): implementation and application
121 -- 132David S. Wishart, Robert F. Boyko, Leigh Willard, Frederic M. Richards, Brian D. Sykes. SEQSEE: a comprehensive program suite for protein sequence analysis
133 -- 135R. G. Duggleby. Calculation of the molecular weight of proteins from electrophoretic and gel exclusion chromatographic experiments
145 -- 151F. Rodriguez, A. Altibelli, A. Lopez. BUILD: a program generator for modelling experimental biological data
153 -- 161H. Cantalloube, C. Nahum, A. Achour, T. Lehner, Isabelle Callebaut, Arsène Burny, B. Bizzini, Jean Paul Mornon, D. Zagury, J. F. Zagury. Automat: a novel software system for the systematic search for protein (or DNA) similarities with a notable application to autoimmune diseases and AIDS
163 -- 169M. Kamimura, Y. Takahashi. Phi-psi conformational pattern clustering of protein amino acid residues using the potential function method
171 -- 178Rainer Fuchs. Predicting protein function: a versatile tool for the Apple Macintosh
185 -- 187J. M. Lacroix. DNA fragment size determination on agarose gel by using the application GEL
189 -- 191Sudhir Kumar, Koichiro Tamura, Masatoshi Nei. MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers
193 -- 197H. Blocker, D. N. Lincoln. The shortmer approach to nucleic acid sequence analysis. I: Computer simulation of sequencing projects to find economical primer sets
199 -- 205Dominic A. Clark, Christopher J. Rawlings. Intelligent Systems for Molecular Biology: review of the first international conference [published erratum appears in Comput Appl Biosci 1994 10(3)]
207 -- 208W. A. Gilbert. FarFetch - an Internet-based sequence entry server
209 -- 210B. K. Tizard, J. A. Stanton, N. G. Laing. DiffScreen: the merging of image subtraction and molecular genetics for the rapid analysis of differentially screened cDNA libraries
211 -- 212A. Laferriere, Daniel Gautheret, Robert Cedergren. An RNA pattern matching program with enhanced performance and portability
213 -- 214O. Gefeller, T. Bregenzer. Computer programs for exact nonparametric inference

Volume 10, Issue 1

3 -- 5A. Torelli, C. A. Robotti. ADVANCE and ADAM: two algorithms for the analysis of global similarity between homologous informational sequences
7 -- 9E. Arakawa, H. Yoshikura, K. Yamamoto. Some features on RNA folding structures of cytochrome c oxidase subunit II and cytochrome P450
11 -- 12Y. Ina. ODEN: a program package for molecular evolutionary analysis and database search of DNA and amino acid sequences
13 -- 17V. B. Fedoseyeva, S. A. Otenko, A. A. Alexndrov. Nucleotide sequence statistical analysis of pauses in RNA elongation by Escherichia coli RNA polymerase
19 -- 29Julie Dawn Thompson, Desmond G. Higgins, Toby J. Gibson. Improved sensitivity of profile searches through the use of sequence weights and gap excision
31 -- 34Reinhard Doelz. Hierarchical Access System for Sequence Libraries in Europe (HASSLE): a tool to access sequence databases remotely
35 -- 39L. Rosenthaler, Reinhard Doelz, L. Tosoni. Simplified user poll and experience report language (SUPER): implementation and application
41 -- 48Gary J. Olsen, Hideo Matsuda, Ray Hagstrom, Ross A. Overbeek. fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood
49 -- 51Frank-Ulrich Gast. A Macintosh program for the versatile generation of random nucleic acid sequences and their structural analysis
53 -- 60Burkhard Rost, Chris Sander, Reinhard Schneider. PHD - an automatic mail server for protein secondary structure prediction
67 -- 70John M. Hancock, John S. Armstrong. SIMPLE34: an improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences
75 -- 77Gisbert Schneider, Tilman Todt, Paul Wrede. De novo design of peptides and proteins: machine-generated sequences by the PROSA program
79 -- 80Rainer Fuchs. Fast protein block searches