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ORCIDComputer Applications in the Biosciences, Volume 13
Volume 13, Number 1, February 1997
- Kathleen M. Currey, Bruce A. Shapiro:
Secondary structure computer prediction of the poliovirus 5' non-coding region is improved by a genetic algorithm. 1-12 - G. Chelvanayagam, Simon Easteal
:
Correlating patterns in alignments of polymorphic sequences with experimental assays. 13-22 - Asaf A. Salamov, Victor V. Solovyev:
Recognition of 3'-processing sites of human mRNA precursors. 23-28 - Q. 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. 29-35 - Eugene V. Korotkov, Maria A. Korotkova, J. S. Tulko:
Latent sequence periodicity of some oncogenes and DNA-binding protein genes. 37-44 - J. Alicia Grice, Richard Hughey, Don Speck:
Reduced space sequence alignment. 45-53 - Benny Shomer:
EMBL sequence submission system--an object-oriented approach to developing interactive data collection systems through the WWW. 55-60 - C. Hoogland, C. Biemont:
DROSOPOSON: a knowledge base on chromosomal localization of transposable element insertions in Drosophila. 61-68 - C. 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. 69-73 - Kun-Mao Chao, Jinghui Zhang, James Ostell, Webb Miller:
A tool for aligning very similar DNA sequences. 75-80 - G. S. Miller, Rainer Fuchs:
Post-processing of BLAST results using databases of clustered sequences. 81-87 - Kornelie Frech, Kerstin Quandt, Thomas Werner:
Software for the analysis of DNA sequence elements of transcription. 89-97 - Michael G. Roberts, David A. Phoenix, Arthur R. Pewsey:
An algorithm for the detection of surface-active alpha helices with the potential to anchor proteins at the membrane interface. 99-106 - William Bains:
Hexanucleotide frequency database. 107-108 - Kornelie Frech, P. Dietze, Thomas Werner:
ConsInspector 3.0: new library and enhanced functionality. 109-110 - Alexis 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. 111-113
Volume 13, Number 2, April 1997
- Alexander 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. 115-122 - J. H. Woods, Herbert M. Sauro:
Elasticities in Metabolic Control Analysis: algebraic derivation of simplified expressions. 123-130 - Eric 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. 131-136 - Eric Glémet, Jean-Jacques Codani:
LASSAP, a LArge Scale Sequence compArison Package. 137-143 - Andrzej Wozniak:
Using video-oriented instructions to speed up sequence comparison. 145-150 - Jacek Blazewicz, Janusz Kaczmarek, Marta Kasprzak, Wojciech T. Markiewicz, Jan Weglarz:
Sequential and parallel algorithms for DNA sequencing. 151-158 - Ramón Varón, Francisco García-Sevilla, Manuela García-Moreno, F. García-Cánovas, R. Peyro, Ronald G. Duggleby:
Computer program for the equations describing the steady state of enzyme reactions. 159-167 - Linton Winder, Martin Lefley, Barbara Smith:
A key for freshwater invertebrates using fuzzy logic. 169-174 - Todd Smith, Chris Abajian, Leroy E. Hood:
Hopper: software for automating data tracking and flow in DNA sequencing. 175-182 - Y. 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. 183-190 - Christian Barrett, Richard Hughey, Kevin Karplus:
Scoring hidden Markov models. 191-199 - L. Cocea:
Search the Human cDNA Database at TIGR. 201-204 - I. Belyi, Pavel A. Pevzner:
Software for DNA sequencing by hybridization. 205-210
Volume 13, Number 3, June 1997
- R. R. Mallios:
An iterative algorithm for converting a class II MHC binding motif into a quantitative predictive model. 211-215 - Prakash M. Nadkarni:
Mapdiff: determining differences between two genomic maps. 217-225 - Yves Van de Peer, Rupert De Wachter:
Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. 227-230 - Patrick Aloy, Juan Cedano, Baldomero Oliva, Francesc X. Avilés, Enrique Querol:
'TransMem': a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins. 231-234 - Andrew Rambaut, Nicholas C. Grassly:
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. 235-238 - Rainer Fuchs:
Grouper - creation of marker sets for multiplexed genotyping. 239-241 - Anatoly S. Frolov, I. S. Pika, A. M. Eroshkin:
ProMSED: protein multiple sequence editor for Windows 3.11/95. 243-248 - Eric Depiereux, Guy Baudoux, Pascal Briffeuil, Isabelle Reginster, Xavier De Bolle, Carla Vinals, Ernest Feytmans:
Match-Box_server: a multiple sequence alignment tool placing emphasis on reliability. 249-256 - Josef Pánek, Jirí Vohradský:
Object-oriented developmental environment for image-analysis applications: implementation for 2D gel electrophoretogram analysis. 257-262 - S. Tiwari, S. Ramachandran, Alok Bhattacharya, S. Bhattacharya, Ramakrishna Ramaswamy:
Prediction of probable genes by Fourier analysis of genomic sequences. 263-270 - Lutz Ehrlich, Christian Münkel, Giuseppe Chirico, Jörg Langowski:
A Brownian dynamics model for the chromatin fiber. 271-279 - S. Panzer, L. Cooley, Perry L. Miller:
Using explicitly represented biological relationships for database navigation and searching via the World-Wide Web. 281-290 - Gilles Labesse, N. Colloc'h, Joël Pothier, J. P. Mornon:
P-SEA: a new efficient assignment of secondary structure from C alpha trace of proteins. 291-295 - András Fiser, Zsuzsanna Dosztányi, István Simon:
The role of long-range interactions in defining the secondary structure of proteins is overestimated. 297-301 - Andrew Rambaut, Paul H. Harvey, Sean Nee:
End-Epi: an application for inferring phylogenetic and population dynamical processes from molecular sequences. 303-306 - Julio Rozas, Ricardo Rozas:
DnaSP version 2.0: a novel software package for extensive molecular population genetics analysis. Comput. Appl. Biosci. 13(3): 307-311 (1997) - Joaquín Dopazo:
A new index to find regions showing an unexpected variability or conservation in sequence alignments. Comput. Appl. Biosci. 13(3): 313-317 (1997) - Florencio Pazos, O. Olmea, Alfonso Valencia:
A graphical interface for correlated mutations and other protein structure prediction methods. Comput. Appl. Biosci. 13(3): 319-321 (1997) - Yasuhiko Wada, K. Inoue, K. Ohga, Hiroshi Yasue:
Software tool for gene mapping: gRanch. Comput. Appl. Biosci. 13(3): 323-324 (1997)
Volume 13, Number 4, August 1997
- William R. Pearson:
Identifying distantly related protein sequences. 325-332 - David B. Searls:
Linguistic approaches to biological sequences. 333-344 - Burkhard Rost, Seán I. O'Donoghue:
Sisyphus and prediction of protein structure. 345-356 - Tatsuya Akutsu, Kentaro Onizuka, Masato Ishikawa:
Rapid protein fragment search using hash functions based on the Fourier transform. 357-364 - Steven Salzberg:
A method for identifying splice sites and translational start sites in eukaryotic mRNA. 365-376 - Jan-Hendrik S. Hofmeyr, Athel Cornish-Bowden:
The reversible Hill equation: how to incorporate cooperative enzymes into metabolic models. 377-385 - Hiroyuki Toh:
Introduction of a distance cut-off into structural alignment by the double dynamic programming algorithm. 387-396 - William Noble Grundy, Timothy L. Bailey, Charles Elkan, Michael E. Baker:
Meta-MEME: motif-based hidden Markov models of protein families. 397-406 - P. 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. 407-413 - Masahiro Ito, Yo Matsuo, Ken Nishikawa:
Prediction of protein secondary structure using the 3D-1D compatibility algorithm. 415-424 - Rob W. W. Hooft, Chris Sander, Gert Vriend:
Objectively judging the quality of a protein structure from a Ramachandran plot. 425-430 - V. Biaudet, Franck Samson, Philippe Bessières:
Micado - a network-oriented database for microbial genomes. 431-438 - Steven Lay, Dennis Bray:
A computer program for the analysis of protein complex formation. 439-444 - J. Schafer, M. Schoniger:
DISTREE: a tool for estimating genetic distances between aligned DNA sequences. 445-451 - Robert W. Gill, T. Charles Hodgman, Chris B. Littler, Marcus D. Oxer, Douglas S. Montgomery, Steve Taylor, Philippe Sanseau:
A new dynamic tool to perform assembly of expressed sequence tags (ESTs). 453-457 - Bruce A. Shapiro, Jin Chu Wu:
Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm. 459-471 - Ross D. King, Mansoor A. S. Saqi, Roger A. Sayle, Michael J. E. Sternberg:
DSC: public domain protein secondary structure predication. 473-474 - L. I. Toldo:
JaMBW 1.1: Java-based Molecular Biologists' Workbench. 475-476 - Richard Mott:
EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA. 477-478 - J. S. Amthor:
Calculation of daylength. 479-480 - Miguel 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. 481-483 - E. Lorenz, S. Leeton, R. J. Owen:
A simple method for sizing large fragments of bacterial DNA separated by PFGE. 485-486
Volume 13, Number 5, October 1997
- Ilya N. Shindyalov, Philip E. Bourne:
Protein data representation and query using optimized data decomposition. 487-496 - S. 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. 497-508 - Inge Jonassen:
Efficient discovery of conserved patterns using a pattern graph. 509-522 - Carol Soderlund, Ian Longden, Richard Mott:
FPC: a system for building contigs from restriction fingerprinted clones. 523-535 - Ronald G. Forsythe Jr., Peter D. Karp, Michael L. Mavrovouniotis:
Estimation of equilibrium constants using automated group contribution methods. 537-543 - Benny Shomer:
Seqalert - a daily sequence alertness server for the EMBL and SWISSPROT databases. 545-547 - Hugh E. Williams, Justin Zobel:
Compression of nucleotide databases for fast searching. 549-554 - Ziheng Yang:
PAML: a program package for phylogenetic analysis by maximum likelihood. 555-556 - W. Gronwald, Robert F. Boyko, Brian D. Sykes:
GSC: a graphical program for NMR chemical shift comparison. 557-558 - Nicholas C. Grassly, Jun Adachi, Andrew Rambaut:
PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees. 559-560 - David S. Wishart, Scott Fortin, David R. Woloschuk, Warren Wong, Timothy Rosborough, Gary H. Van Domselaar, Jonathan Schaeffer, Duane Szafron:
A platform-independent graphical user interface for SEQSEE and XALIGN. 561-562 - Jean-Paul Rolland, Patrick Bon, Daniel Thomas:
MACS: automatic counting of objects based on shape recognition. 563-564
Volume 13, Number 6, December 1997
- Ching Zhang, Andrew K. C. Wong:
A genetic algorithm for multiple molecular sequence alignment. 565-581 - Jan Gorodkin, Laurie J. Heyer, Søren Brunak, Gary D. Stormo:
Displaying the information contents of structural RNA alignments: the structure logos. 583-586 - P. A. Doris, A. Hayward-Lester, J. K. Hays Sr.:
Q-RT-PCR: data analysis software for measurement of gene expression by competitive RT-PCR. 587-591 - Hiroaki Kato, Yoshimasa Takahashi:
SS3D-P2: a three dimensional substructure search program for protein motifs based on secondary structure elements. 593-600 - Jérôme Gouzy, P. Eugène, Elizabeth A. Greene, Daniel Kahn, Florence Corpet:
XDOM, a graphical tool to analyse domain arrangements in any set of protein sequences. 601-608 - Pascale Guerdoux-Jamet, Dominique Lavenier:
SAMBA: hardware accelerator for biological sequence comparison. 609-615 - David Fenyö:
A software tool for the analysis of mass spectrometric disulfide mapping experiments. 617-618 - Hedvig Hegyi, J. M. Lai, Peer Bork:
The Sequence Alerting Server - a new WEB server. 619-620 - Thomas Sicheritz-Pontén:
BioWish: a molecular biology command extension to Tcl/Tk. 621-622 - A. S. Law, D. W. Burt:
Two applications to facilitate the viewing of database search result files on the Macintosh. 623-624 - Jens Stoye, Vincent Moulton, Andreas W. M. Dress:
DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment. 625-626
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