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ORCIDComputer Applications in the Biosciences, Volume 10
Volume 10, Number 1, February 1994
- A. Torelli, C. A. Robotti:
ADVANCE and ADAM: two algorithms for the analysis of global similarity between homologous informational sequences. 3-5 - Eiji Arakawa, Hiroshi Yoshikura, Kenji Yamamoto:
Some features on RNA folding structures of cytochrome c oxidase subunit II and cytochrome P450. 7-9 - Yasuo Ina:
ODEN: a program package for molecular evolutionary analysis and database search of DNA and amino acid sequences. 11-12 - V. B. Fedoseyeva, S. A. Otenko, A. A. Alexndrov:
Nucleotide sequence statistical analysis of pauses in RNA elongation by Escherichia coli RNA polymerase. 13-17 - Julie Dawn Thompson, Desmond G. Higgins, Toby J. Gibson
:
Improved sensitivity of profile searches through the use of sequence weights and gap excision. 19-29 - Reinhard Doelz:
Hierarchical Access System for Sequence Libraries in Europe (HASSLE): a tool to access sequence databases remotely. 31-34 - L. Rosenthaler, Reinhard Doelz, L. Tosoni:
Simplified user poll and experience report language (SUPER): implementation and application. 35-39 - Gary J. Olsen, Hideo Matsuda, Ray Hagstrom, Ross A. Overbeek:
fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. 41-48 - Frank-Ulrich Gast:
A Macintosh program for the versatile generation of random nucleic acid sequences and their structural analysis. 49-51 - Burkhard Rost, Chris Sander, Reinhard Schneider:
PHD - an automatic mail server for protein secondary structure prediction. 53-60 - J. Jursa:
DNA modeller: an interactive program for modelling stacks of DNA base pairs on a microcomputer. 61-65 - John 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. 67-70 - M. P. Maradona:
Integrated software for probabilistic identification of microorganisms. 71-73 - Gisbert Schneider, Tilman Todt, Paul Wrede:
De novo design of peptides and proteins: machine-generated sequences by the PROSA program. 75-77 - Rainer Fuchs:
Fast protein block searches. 79-80
Volume 10, Number 2, April 1994
- Michael Levin:
A Julia set model of field-directed morphogenesis: developmental biology and artificial life. 85-103 - L. Rosenthaler, Reinhard Doelz:
Simplified user poll and experience report language (SUPER): implementation and application. 105-109 - M. S. Chapman:
Sequence similarity scores and the inference of structure-function relationships. 111-119 - David S. Wishart, Robert F. Boyko, Leigh Willard, Frederic M. Richards, Brian D. Sykes:
SEQSEE: a comprehensive program suite for protein sequence analysis. 121-132 - R. G. Duggleby:
Calculation of the molecular weight of proteins from electrophoretic and gel exclusion chromatographic experiments. 133-135 - P. J. Monardo, T. Boutell, J. I. Garrels, G. I. Latter:
A distributed system for two-dimensional gel analysis. 137-143 - Frédéric Rodriguez, Anne Altibelli, André Lopez:
BUILD: a program generator for modelling experimental biological data. 145-151 - Hubert Cantalloube, Carole E. Nahum, A. Achour, T. Lehner, Isabelle Callebaut, Arsène Burny, B. Bizzini, Jean Paul Mornon, D. Zagury, Jean-François Zagury:
Automat: a novel software system for the systematic search for protein (or DNA) similarities with a notable application to autoimmune diseases and AIDS. 153-161 - Motokazu Kamimura, Yoshimasa Takahashi:
Phi-psi conformational pattern clustering of protein amino acid residues using the potential function method. 163-169 - Rainer Fuchs:
Predicting protein function: a versatile tool for the Apple Macintosh. 171-178 - K. U. Frohlich:
Sequence Similarity Presenter: a tool for the graphic display of similarities of long sequences for use in presentations. 179-183 - Jean-Michel Lacroix:
DNA fragment size determination on agarose gel by using the application GEL. 185-187 - Sudhir Kumar, Koichiro Tamura, Masatoshi Nei:
MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. 189-191 - H. Blocker, D. N. Lincoln:
The 'shortmer' approach to nucleic acid sequence analysis. I: Computer simulation of sequencing projects to find economical primer sets. 193-197 - Dominic 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)]. 199-205 - William A. Gilbert:
FarFetch - an Internet-based sequence entry server. 207-208 - B. K. Tizard, Jo-Ann Stanton, N. G. Laing:
DiffScreen: the merging of image subtraction and molecular genetics for the rapid analysis of differentially screened cDNA libraries. 209-210 - A. Laferriere, Daniel Gautheret, Robert Cedergren:
An RNA pattern matching program with enhanced performance and portability. 211-212 - Olaf Gefeller, T. Bregenzer:
Computer programs for exact nonparametric inference. 213-214
Volume 10, Number 3, June 1994
- X. Huang:
An algorithm for identifying regions of a DNA sequence that satisfy a content requirement. 219-225 - X. Huang:
On global sequence alignment. 227-235 - G. A. Lambert:
Software-controlled testing for antidromic activation of single neurones. 237-241 - B. Golding:
Exploratory analysis of multiple sequence alignments using phylogenies. 243-247 - James A. Inglehart, Peter C. Nelson:
On the limitations of automated restriction mapping. 249-261 - Elias Zintzaras, Nigel P. Brown, Axel Kowald:
Growing a classification tree using the apparent misclassification rate. 263-271 - F. Dardel:
MC-Fit: using Monte-Carlo methods to get accurate confidence limits on enzyme parameters. 273-275 - Fabio E. Penotti:
A distributed system for DNA/protein database similarity searches. 277-280 - P. R. Reeves, Leslie Farnell, Ruiting Lan:
MULTICOMP: a program for preparing sequence data for phylogenetic analysis. 281-284 - Malcolm 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. 285-294 - E. 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. 295-299 - Erik L. L. Sonnhammer, Richard Durbin:
A workbench for large-scale sequence homology analysis. 301-307 - Peisen Zhang, Eric A. Schon, Stuart G. Fischer, Eftihia Cayanis, Janie Weiss, Susan Kistler, Philip E. Bourne:
An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA. 309-317 - Victor B. Strelets, Andrey A. Ptitsyn, Luciano Milanesi, Hwa A. Lim:
Data bank homology search algorithm with linear computation complexity. 319-322 - W. G. Hoeck:
InfoTrac TFD: a microcomputer implementation of the Transcription Factor Database TFD with a graphical user interface. 323-327 - T. N. Bryant:
A bacterial identification teaching exercise revisited. 329-334 - S. A. Sammons, D. P. Dykes:
OLGCG: an OPEN LOOK interface to the GCG sequence analysis package. 335-339 - L. B. Ellis, R. P. Milius:
Valid and invalid implementations of GOR secondary structure predictions. 341-348 - Carol Soderlund, Christian Burks:
GRAM and genfragII: solving and testing the single-digest, partially ordered restriction map problem. 349-358 - T. N. Bryant:
A program for reordering coded data. 359-360 - Prakash M. Nadkarni, Stephen T. Reeders, Jing Zhou:
A modification of the ALIGN program to assist visual interpretation of mutated sequences. 361-362
Volume 10, Number 4, July 1994
- K. W. Hart, David B. Searls, G. Christian Overton:
SORTEZ: a relational translator for NCBI's ASN.1 database. 369-378 - Osamu Gotoh:
Further improvement in methods of group-to-group sequence alignment with generalized profile operations. 379-387 - Florence Corpet, B. Michot:
RNAlign program: alignment of RNA sequences using both primary and secondary structures. 389-399 - A. Gleizes, Alain Hénaut:
A global approach for contig construction. 401-408 - Andrey Rzhetsky, Masatoshi Nei:
METREE: a program package for inferring and testing minimum-evolution trees. 409-412 - Rainer Fuchs:
Sequence analysis by electronic mail: a tool for accessing Internet e- mail servers. 413-417 - Jin Kim, Sakti Pramanik, Moon-Jung Chung:
Multiple sequence alignment using simulated annealing. 419-426 - C. S. Tung, Eugene S. Carter II:
Nucleic acid modeling tool (NAMOT): an interactive graphic tool for modeling nucleic acid structures. 427-433 - L. W. Wright, J. B. Lichter, John Reinitz, Mark A. Shifman, Kenneth K. Kidd, Perry L. Miller:
Computer-assisted restriction mapping: an integrated approach to handling experimental uncertainty. 435-442 - Andrew Fire:
A four-dimensional digital image archiving system for cell lineage tracing and retrospective embryology. 443-447 - M. R. Mautino:
A computer program for construction of circular restriction maps. 449-452 - Claudine Landes, Jean-Loup Risler:
Fast databank searching with a reduced amino-acid alphabet. 453-454 - Webb Miller, Mark Boguski:
A note about computing all local alignments. 455-456 - Roman L. Tatusov, Eugene V. Koonin:
A simple tool to search for sequence motifs that are conserved in BLAST outputs. 457-459
Volume 10, Number 5, September 1994
- Chiara Scapoli, A. Rodriguez-Larralde, Stefano Volinia, M. Beretta, Italo Barrai:
Identification of a set of frequent decanucleotides in plants and in animals. 465-470 - Dennis Bray, Steven Lay:
Rapid numerical integration algorithm for finding the equilibrium state of a system of coupled binding reactions. 471-476 - Mondher Farza, Arlette Chéruy:
BIOESTIM: software for automatic design of estimators in bioprocess engineering. 477-488 - Carlo 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. 489-494 - J. Clotet, Juan Cedano, Enrique Querol:
An Excel spreadsheet computer program combining algorithms for prediction of protein structural characteristics. 495-500 - Roberto Gambari, Stefano Volinia, Carlo Nesti, Chiara Scapoli, Italo Barrai:
A set of Alu-free frequent decamers from mammalian genomes enriched in transcription factor signals. 501-508 - Oswaldo Trelles-Salazar, Emilio L. Zapata, José María Carazo:
On an efficient parallelization of exhaustive sequence comparison algorithms on message passing architectures. 509-511 - Y. Elkind, B. Nir, Joel Ira Weller:
Maximum likelihood estimation of quantitative trait loci parameters with the aid of genetic markers using a standard statistical package. 513-517 - Klaus Heumann, David G. George, Hans-Werner Mewes:
A new concept of sequence data distribution on wide area networks. 519-526 - L. A. Parodi, C. A. Granatir, Gerald M. Maggiora:
A consensus procedure for predicting the location of alpha-helical transmembrane segments in proteins. 527-535 - Janos Posfai, Z. Szaraz, Richard J. Roberts:
VISA: Visual Sequence Analysis for the comparison of multiple amino acid sequences. 537-544 - Mansoor A. S. Saqi, Roger A. Sayle:
PdbMotif--a tool for the automatic identification and display of motifs in protein structures. 545-546 - Kenta Nakai, T. Tokimori, A. Ogiwara, Ikuo Uchiyama, T. Niiyama:
Gnome - an Internet-based sequence analysis tool. 547-550 - L. L. Walsh:
Navigating the Brookhaven Protein Data Bank. 551-557 - J. Altimiras, M. Feliu, A. Aissaoui, Lluis Tort:
Computing heart rate variability using spectral analysis techniques: HRVUAB, a ready-to-use program. 559-562 - J. T. Niemi, P. Mantsala:
TRACTOR, a program to locate subclones in a nucleotide sequence using only one sequencing reaction. 563-566 - Michael L. Engle, Christian Burks:
GenFrag 2.1: new features for more robust fragment assembly benchmarks. 567-568 - Yves 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. 569-570
Volume 10, Number 6, December 1994
- Weider Chang, Ilya N. Shindyalov, Calton Pu, Philip E. Bourne:
Design and application of PDBlib, a C++ macromolecular class library. 575-586 - Adam Godzik, Jeffrey Skolnick:
Flexible algorithm for direct multiple alignment of protein structures and sequences. 587-596 - Yury V. Kondrakhin, V. V. Shamin, Nikolay A. Kolchanov:
Construction of a generalized consensus matrix for recognition of vertebrate pre-mRNA 3'-terminal processing sites. 597-603 - V. A. Shepelev, N. V. Yanishevsky:
Multidimensional dot-matrices. 605-611 - Ying Xu, Richard J. Mural, Edward C. Uberbacher:
Constructing gene models from accurately predicted exons: an application of dynamic programming. 613-623 - Yuhong Wang, Rolf A. Prade, James Griffith, William E. Timberlake, Jonathan P. Arnold:
ODS_BOOTSTRAP: assessing the statistical reliability of physical maps by bootstrap resampling. 625-634 - Gisbert Schneider, Johannes Schuchhardt, Paul Wrede:
Artificial neural networks and simulated molecular evolution are potential tools for sequence-oriented protein design. 635-645 - Pankaj Agarwal:
Simulation of aggregation in Dictyostelium using the Cell Programming Language. 647-655 - T. N. Bryant:
Identifying correct bacteriological vocabulary: software to look up RKC codes and statements. 657-660 - Victor V. Solovyev, Asaf A. Salamov:
Predicting alpha-helix and beta-strand segments of globular proteins. 661-669 - Steven W. Smith, Ross A. Overbeek, Carl R. Woese, W. Gilbert, P. M. Gillevet:
The genetic data environment an expandable GUI for multiple sequence analysis. 671-675 - M. L. Cain, L. W. Murray:
Non-linear regression models to estimate the size of DNA fragments. 677-680 - S. R. Wilson, P. J. Solomon:
Estimates for different stages of HIV/AIDS disease. 681-683 - M. Gonzalo Claros, Gunnar von Heijne:
TopPred II: an improved software for membrane protein structure predictions. 685-686 - David S. Wishart, Robert F. Boyko, Brian D. Sykes:
Constrained multiple sequence alignment using XALIGN. 687-688
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