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ORCIDComputer Applications in the Biosciences, Volume 12
Volume 12, Number 1, February 1996
- Giorgio Grillo, Marcella Attimonelli, Sabino Liuni, Graziano Pesole:
CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases. 1-8 - Malcolm 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. 9-18 - Sridhar Hannenhalli, William Feldman, Herbert F. Lewis, Steven Skiena
, Pavel A. Pevzner:
Positional sequencing by hybridization. 19-24 - Eugene S. Carter II, C. S. Tung:
NAMOT2 - a redesigned nucleic acid modeling tool: construction of non-canonical DNA structures. 25-30 - Xiaojun Guan, Edward C. Uberbacher:
Alignments of DNA and protein sequences containing frameshift errors. 31-40 - Piero Fariselli, Rita Casadio:
HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins. 41-48 - Vsevolod J. Makeev, Vladimir G. Tumanyan:
Search of periodicities in primary structure of biopolymers: a general Fourier approach. 49-54 - A. Nandy:
Two-dimensional graphical representation of DNA sequences and intron-exon discrimination in intron-rich sequences. 55-62 - Guy Perrière, Jean Thioulouse:
On-line tools for sequence retrieval and multivariate statistics in molecular biology. 63-69 - Franz Wolfertstetter, Kornelie Frech, Grit Herrmann, Thomas Werner:
Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm. 71-80
Volume 12, Number 2, April 1996
- Carlo 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. 81-88 - D. N. Perkins, Terri K. Attwood:
XFINGER: a tool for searching and visualising protein fingerprints and patterns. 89-94 - Richard Hughey, Anders Krogh:
Hidden Markov models for sequence analysis: extension and analysis of the basic method. 95-107 - Cathy H. Wu, Sheng Zhao, Hsi-Lien Chen, Chin-Ju Lo, Jerry McLarty:
Motif identification neural design for rapid and sensitive protein family search. 109-118 - Wolfgang Vahrson, Klaus Hermann, Jürgen Kleffe, Burghardt Wittig:
Object-oriented sequence analysis: SCL - a C++ class library. 119-127 - F. Eggenberger, Nicole Redaschi, Reinhard Doelz:
FastAlert - an automatic search system to alert about new entries in biological sequence databanks. 129-133 - Jorja G. Henikoff, Steven Henikoff:
Using substitution probabilities to improve position-specific scoring matrices. 135-143 - D. Curtis Jamison, Brad Mills, Bruce R. Schatz:
An extensible network query unification system for biological databases. 145-150 - G. Schaftenaar, K. Cuelenaere, Jan H. Noordik, Thure Etzold:
A Tcl-based SRS v.4 interface. 151-155 - Dan S. Prestridge:
SIGNAL SCAN 4.0: additional databases and sequence formats. 157-160
Volume 12, Number 3, June 1996
- Igor B. Rogozin, Luciano Milanesi, Nikolay A. Kolchanov:
Gene structure prediction using information on homologous protein sequence. 161-170 - Bruce A. Shapiro, Jin Chu Wu:
An annealing mutation operator in the genetic algorithms for RNA folding. 171-180 - A. S. Law, D. W. Burt:
qValue - a program to calculate comparative measures of genomic reorganisation from cytogenetic and/or linkage information. 181-183 - John A. Byers:
TAXOKEY: a universal taxonomic key program using DOS text files and graphics. 185-189 - Raj K. Singh, D. L. Hoffman, Stephen G. Tell, C. Thomas White:
BioSCAN: a network sharable computational resource for searching biosequence databases. 191-196 - Grit Herrmann, Astrid Schön, R. Brack-Werner, Thomas Werner:
CONRAD: a method for identification of variable and conserved regions within proteins by scale-space filtering. 197-203 - Akihiro Nakaya, Kenjiro Taura, Kenji Yamamoto, Akinori Yonezawa:
Visualization of RNA secondary structures using highly parallel computers. 205-211 - Shigehiko Kanaya, Yoshihiro 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. 213-225 - Jürgen Sühnel:
Image library of biological macromolecules. 227-229 - Y. Wada, H. Yasue:
Development of an animal genome database and its search system. 231-235 - Kirill Degtyarenko, Péter Fábián:
The directory of P450-containing systems on WorldWide Web. 237-240 - Jean-Paul Rolland, Mohamed J. Flifla, Mireille Garreau, Daniel Thomas:
IBIS version 3: an OSF/Motif-based interface for IBIS - integrated biological imaging system. 241-245 - O. Matzura, A. Wennborg:
RNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows. 247-249 - Ross D. King, C. G. Angus:
PM - protein music. 251-252 - Vitali Proutski, Edward C. Holmes:
Primer Master: a new program for the design and analysis of PCR primers. 253-255 - B. I. Osborne:
Three sets of Macintosh AppleScripts for the automatic submission of sequence data to the internet BLAST server. 257-258
Volume 12, Number 4, August 1996
- Jin Kim, James R. Cole, Sakti Pramanik:
Alignment of possible secondary structures in multiple RNA sequences using simulated annealing. 259-267 - Suchendra M. Bhandarkar, Sridhar Chirravuri, Jonathan P. Arnold:
PARODS - a study of parallel algorithms for ordering DNA sequences. 269-280 - Klaus Lindauer, Cezar Bendic, Jürgen Sühnel:
HBexplore - a new tool for identifying and analysing hydrogen bonding patterns in biological macromolecules. 281-289 - Ingrid B. Jakobsen, Simon Easteal:
A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. 291-295 - Igor Kuznetsov, Pavel Morozov:
GEOMETRY: a software package for nucleotide sequence analysis using statistical geometry in sequence space. 297-301 - William Noble Grundy, Timothy L. Bailey, Charles Elkan:
ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool. 303-310 - Lijuan Hu, Elaine F. Saulinskas, Peter Johnson, Peter de B. Harrington:
Development of an expert system for amino acid sequence identification. 311-318 - Cheng Che Chen, Richard O. Chen, Russ B. Altman:
Constraining volume by matching the moments of a distance distribution. 319-326 - Kimmen 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. 327-345 - Joël-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. 347-351 - M. P. Maradona:
Software for microbial fingerprinting by means of the infrared spectra. 353-356 - Roderic D. M. Page:
TreeView: an application to display phylogenetic trees on personal computers. 357-358
Volume 12, Number 5, October 1996
- Philipp Bucher, James W. Fickett, Artemis G. Hatzigeorgiou:
Computational analysis of transcriptional regulatory elements: a field in flux. 361-362 - C. Fondrat, A. Kalogeropoulos:
Approaching the function of new genes by detection of their potential upstream activation sequences in Saccharomyces cerevisiae: application to chromosome III. 363-374 - Craig J. Benham:
Computation of DNA structural variability - a new predictor of DNA regulatory regions. 375-381 - Alexander 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. 383-389 - Gordon B. Hutchinson:
The prediction of vertebrate promoter regions using differential hexamer frequency analysis. 391-398 - Luciano Milanesi, Marco Muselli, P. Arrigo:
Hamming-Clustering method for signals prediction in 5' and 3' regions of eukaryotic genes. 399-404 - Kerstin Quandt, Korbinian Grote, Thomas Werner:
GenomeInspector: a new approach to detect correlation patterns of elements on genomic sequences. 405-413 - David A. Rosenblueth, Denis Thieffry, Araceli M. Huerta, Heladia Salgado, Julio Collado-Vides:
Syntactic recognition of regulatory regions in Escherichia coli. 415-422 - Edward N. Trifonov:
Interfering contexts of regulatory sequence elements. 423-429 - Jean-Michel Claverie, Stéphane Audic:
The statistical significance of nucleotide position-weight matrix matches. 431-439 - Holger Karas, Rainer Knüppel, Wolfgang Schulz, Heinz Sklenar, Edgar Wingender:
Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements. 441-446
Volume 12, Number 6, December 1996
- Jens Hanke, Jens G. Reich:
Kohonen map as a visualization tool for the analysis of protein sequences: multiple alignments, domains and segments of secondary structures. 447-454 - Frédéric Hospital, Christine Dillmann, A. E. Melchinger:
A general algorithm to compute multilocus genotype frequencies under various mating systems. 455-462 - Gilles Labesse:
MulBlast 1.0: a multiple alignment of BLAST output to boost protein sequence similarity analysis. 463-467 - Andrew Rambaut, Nicholas C. Grassly, Sean Nee, Paul H. Harvey:
Bi-De: an application for simulating phylogenetic processes. 469-471 - Richard Hughey:
Parallel hardware for sequence comparison and alignment. 473-479 - Joel Wallman, Guy A. Hoelzer, Don J. Melnick:
The effects of social structure, geographical structure, and population size on the evolution of mitochondrial DNA: I. A simulation model. 481-489 - U. S. Murty, K. Jamil, D. Krishna, P. J. Reddy:
Rule-based system for the fast identification of species of Indian Anopheline mosquitoes. 491-495 - X. Huang, J. Zhang:
Methods for comparing a DNA sequence with a protein sequence. 497-506 - Laurent Duret, Elisabeth Gasteiger, Guy Perrière:
LALNVIEW: a graphical viewer for pairwise sequence alignments. 507-510 - Ying Xu, Edward C. Uberbacher:
A polynomial-time algorithm for a class of protein threading problems. 511-517 - Guy Perrière, J. R. Lobry, Jean Thioulouse:
Correspondence discriminant analysis: a multivariate method for comparing classes of protein and nucleic acid sequences. 519-524 - Rob W. W. Hooft, Chris Sander, Michael Scharf, Gert Vriend:
The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value. 525-529 - Salvatore Lanzavecchia, L. Tosoni, Pier Luigi Bellon:
Fast sinogram computation and the sinogram-based alignment of images. 531-537 - W. J. Heitler:
A simple method for the removal of mains interference from pre-recorded electrophysiological data. 539-542 - Nicolas Galtier, Manolo Gouy, Christian Gautier:
SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. 543-548 - L. Tosoni, Salvatore Lanzavecchia, Pier Luigi Bellon:
Image and volume data rotation with 1- and 3-pass algorithms. 549-552 - Jadranka Lazovic:
Selection of amino acid parameters for Fourier transform-based analysis of proteins. 553-562
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