Nucleic Acids Research, Volume 12

Volume 12, Number 1, January 1984

• Scott Meyers, Peter Friedland:
  Knowledge-based simulation of genetic regulation in bacteriophage lambda. 1-9
  
• René Bach, Yumi Iwasaki, Peter Friedland:
  Intelligent computational assistance for experiment design. 11-29
  
• Catherine Papanicolaou, Manolo Gouy, Jacques Ninio:
  An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules. 31-44
  
• A. B. Jacobson, L. Good, J. Simonetti, Michael Zuker:
  Some simple computational methods to improve the folding of large RNAs. 45-52
  
• Eliahu Comay, Ruth Nussinov, Oded Comay:
  An accelerated algorithm for calculating the secondary structure of single stranded RNAs. 53-66
  
• Paulien Hogeweg, Ben Hesper:
  Energy directed folding of RNA sequences. 67-74
  
• Bruce A. Shapiro, Jacob V. Maizel, Lewis E. Lipkin, Kathleen M. Currey, Colin G. Whitney:
  Generating non-overlapping displays of nucleic acid secondary structure. 75-88
  
• Satoru Kuhara, Fumihiro Matsuo, Shouichi Futamura, A. Fujita, Takeshi Shinohara, Toshihisa Takagi, Yasubumi Sakaki:
  GENAS: a database system for nucleic acid sequence analysis. 89-99
  
• Katsumi Isono:
  A computer program package for storing and retrieving DNA/RNA and protein sequence data. 101-112
  
• Manfred Kröger, Anneliese Kröger-Block:
  Extension of a flexible computer program for handling DNA sequence data. 113-120
  
• Manolo Gouy, F. Milleret, C. Mugnier, M. Jacobzone, Christian Gautier:
  ACNUC: a nucleic acid sequence data base and analysis system. 121-127
  
• Thomas D. Schneider, Gary D. Stormo, M. A. Yarus, L. Gold:
  Delila system tools. 129-140
  
• J. M. Sobieski, K. N. Chen, J. C. Filiatreau, M. H. Pickett, George E. Fox:
  16S rRNA oligonucleotide catalog data base. 141-148
  
• Minoru Kanehisa, James W. Fickett, W. B. Goad:
  A relational database system for the maintenance and verification of the Los Alamos sequence library. 149-158
  
• Verner Paetkau:
  A new rule for analyzing homologous coding sequences in DNA. 159-173
  
• James W. Fickett:
  Fast optimal alignment. 175-179
  
• J. F. Collins, A. F. Coulson:
  Applications of parallel processing algorithms for DNA sequence analysis. 181-192
  
• Manfred Kröger, Anneliese Kröger-Block:
  Simplified computer programs for search of homology within nucleotide sequences. 193-201
  
• Minoru Kanehisa:
  Use of statistical criteria for screening potential homologies in nucleic acid sequences. 203-213
  
• David J. Lipman, W. John Wilbur, Temple F. Smith, Michael S. Waterman:
  On the statistical significance of nucleic acid similarities. 215-226
  
• G. Polner, L. Dorgai, L. Orosz:
  PMAP, PMAPS: DNA physical map constructing programs. 227-236
  
• Michael S. Waterman, Temple F. Smith, H. L. Katcher:
  Algorithms for restriction map comparisons. 237-242
  
• Jiri Novotny, Charles Auffray:
  A program for prediction of protein secondary structure from nucleotide sequence data: application to histocompatibility antigens. 243-255
  
• A. Salemme, A. V. Furano:
  A convenient method for locating sets of related short sequences in DNA sequences of any length. 257-262
  
• R. M. Abarbanel, Paul R. Wieneke, E. Mansfield, David A. Jaffe, Douglas L. Brutlag:
  Rapid searches for complex patterns in biological molecules. 263-280
  
• G. Pierno, N. Barni, M. Candurro, M. Cipollaro, A. Franze, L. Juliano, M. F. Macchiato, G. Mastrocinque, C. Moscatelli, V. Scarlato:
  Computer programs for the characterization of protein coding genes. 281-285
  
• Philipp Bucher, B. Bryan:
  Signal search analysis: a new method to localize and characterize functionally important DNA sequences. 287-305
  
• Hannu Peltola, Hans Söderlund, Esko Ukkonen:
  SEQAID: a DNA sequence assembling program based on a mathematical model. 307-321
  
• H. M. Martinez:
  An RNA folding rule. 323-334
  
• K. Yamamoto, Y. Kitamura, H. Yoshikura:
  Computation of statistical secondary structure of nucleic acids. 335-346
  
• G. J. Quigley, L. Gehrke, D. A. Roth, Philip E. Auron:
  Computer-aided nucleic acid secondary structure modeling incorporating enzymatic digestion data. 347-366
  
• T. W. Stone, K. N. Potter:
  A DNA analysis program designed for computer novices working in an industrial-research environment. 367-378
  
• C. Keller, M. Corcoran, R. J. Roberts:
  Computer programs for handling nucleic acid sequences. 379-386
  
• J. Devereux, P. Haeberli, O. Smithies:
  A comprehensive set of sequence analysis programs for the VAX. 387-395
  
• Jean-Michel Claverie:
  A common philosophy and FORTRAN 77 software package for implementing and searching sequence databases. 397-407
  
• A. H. Reisner, C. A. Bucholtz:
  Utilization of sequence libraries on a 16-bit mini computer with particular reference to high speed searching. 409-416
  
• Minoru Kanehisa, P. Klein, P. Greif, Charles DeLisi:
  Computer analysis and structure prediction of nucleic acids and proteins. 417-428
  
• D. M. Lonsdale, T. P. Hodge, P. J. Stoehr:
  A computer program for the management of small cosmid banks. 429-436
  
• S. Lombardi, H. Seidell, S. Pulford, W. Dutton, S. Parekh:
  Computer programs in nucleic acid synthesis: synthetic strategy development using solid-phase chemical techniques with data storage, retrieval and analysis capabilities. 437-446
  
• P. Taylor:
  A fast homology program for aligning biological sequences. 447-455
  
• D. R. Boswell, A. D. McLachlan:
  Sequence comparison by exponentially-damped alignment. 457-464
  
• B. N. Stone, G. L. Griesinger, J. L. Modelevsky:
  PLASMAP: an interactive computational tool for storage, retrieval and device-independent graphic display of conventional restriction maps. 465-471
  
• A. J. Gray, D. E. Beecher, M. V. Olson:
  Computer-based image analysis of one-dimensional electrophoretic gels used for the separation of DNA restriction fragments. 473-491
  
• P. J. Russell, Richard E. Crandall, R. Feinbaum:
  GELYSIS: Pascal-implemented analysis of one-dimensional electrophoresis gels. 493-498
  
• Rodger Staden:
  A computer program to enter DNA gel reading data into a computer. 499-503
  
• Rodger Staden:
  Computer methods to locate signals in nucleic acid sequences. 505-519
  
• Rodger Staden:
  Graphic methods to determine the function of nucleic acid sequences. 521-538
  
• Michael Gribskov, J. Devereux, R. R. Burgess:
  The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression. 539-549
  
• Rodger Staden:
  Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes. 551-567
  
• B. Malthiery, B. Bellon, D. Giorgi, B. Jacq:
  Apple II PASCAL programs for molecular biologists. 569-579
  
• C. Queen, L. J. Korn:
  A comprehensive sequence analysis program for the IBM personal computer. 581-599
  
• W. F. Schwindinger, J. R. Warner:
  DNA sequence analysis on the IBM-PC. 601-604
  
• L. M. Lagrimini, S. T. Brentano, J. E. Donelson:
  A DNA sequence analysis package for the IBM personal computer. 605-614
  
• Frederick R. Blattner, J. L. Schroeder:
  A computer package for DNA sequence analysis. 615-617
  
• J. S. De Banzie, Evan W. Steeg, J. T. Lis:
  Update for users of the Cornell sequence analysis package. 619-625
  
• P. A. Biro:
  DNA sequence handling programs in BASIC for home computers. 627-631
  
• Andrew Lyall, Peter Hammond, D. Brough, D. Glover:
  BIOLOG - a DNA sequence analysis system in PROLOG. 633-642
  
• J. Pustell, F. C. Kafatos:
  A convenient and adaptable package of computer programs for DNA and protein sequence management, analysis and homology determination. 643-655
  
• M. Johnsen:
  JINN, an integrated software package for molecular geneticists. 657-664
  
• V. A. Luckow, R. K. Littlewood, R. H. Rownd:
  Interactive computer programs for the graphic analysis of nucleotide sequence data. 665-673
  
• M. Komaromy, H. Govan:
  An inexpensive semi-automated sequence reader for the Apple II computer. 675-678
  
• T. Kieser:
  DNAGEL: a computer program for determining DNA fragment sizes using a small computer equipped with a graphics tablet. 679-688
  
• J. I. Rood, J. M. Gawthorne:
  Apple software for analysis of the size of restriction fragments. 689-694
  
• Claude V. Maina, Gary P. Nolan, Aladar A. Szalay:
  Molecular weight determination program. 695-702
  
• R. Durand, F. Bregegere:
  An efficient program to construct restriction maps from experimental data with realistic error levels. 703-716
  
• Gary P. Nolan, Claude V. Maina, Aladar A. Szalay:
  Plasmid mapping computer program. 717-729
  
• P. R. Caron:
  KLONER; a computer program to simulate recombinant DNA strategies by restriction map manipulation. 731-737
  
• D. Shalloway, N. R. Deering:
  Recombinant DNA data management at the restriction and functional site level. 739-750
  
• C. Thomas White, S. C. Hardies, C. A. Hutchison III, M. H. Edgell:
  The diagonal-traverse homology search algorithm for locating similarities between two sequences. 751-766
  
• S. E. Zweig:
  Analysis of large nucleic acid dot matrices on small computers. 767-776
  
• R. Arentzen, W. C. Ripka:
  Introduction of restriction enzyme sites in protein-coding DNA sequences by site-specific mutagenesis not affecting the amino acid sequence: a computer program. 777-787
  
• M. E. Mulligan, D. K. Hawley, R. Entriken, W. R. McClure:
  Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. 789-800
  
• K. Watanabe, K. Yasukawa, K. Iso:
  Graphic display of nucleic acid structure by a microcomputer. 801-809
  
• David W. Mount, Bruce Conrad:
  Microcomputer programs for graphic analysis of nucleic acid and protein sequences. 811-817
  
• David W. Mount, Bruce Conrad:
  Microcomputer programs for back translation of protein to DNA sequences and analysis of ambiguous DNA sequences. 819-823
  
• J. K. Vass, R. H. Wilson:
  'ZSTATS' - a statistical analysis for potential Z-DNA sequences. 825-832
  
• R. E. Raupach:
  Computer programs used to aid in the selection of DNA hybridization probes. 833-836
  
• J. H. Yang, J. H. Ye, Douglas C. Wallace:
  Computer selection of oligonucleotide probes from amino acid sequences for use in gene library screening. 837-843
  
• E. J. Gough, N. M. Gough:
  Direct calculation of the sizes of DNA fragments separated by gel electrophoresis using programmes written for a pocket calculator. 845-853
  

Volume 12, Number 13, July 1984

• M. Nelson, C. Christ, I. Schildkraut:
  Alteration of apparent restriction endonuclease recognition specificities by DNA methylases. 5165-5173
  
• R. Diaz, S. Ortega:
  Initiation of plasmid R1 replication in vitro is independent of transcription by host RNA polymerase. 5175-5191
  
• S. Searle, D. A. Gillespie, D. J. Chiswell, J. A. Wyke:
  Analysis of the variations in proviral cytosine methylation that accompany transformation and morphological reversion in a line of Rous sarcoma virus-infected Rat-1 cells. 5193-5210
  
• P. Valentin-Hansen, K. Hammer, J. E. Love Larsen, I. Svendsen:
  The internal regulated promoter of the deo operon of Escherichia coli K- 12. 5211-5224
  
• H. Nomiyama, T. Tsuzuki, S. Wakasugi, M. Fukuda, K. Shimada:
  Interruption of a human nuclear sequence homologous to mitochondrial DNA by a member of the KpnI 1.8 kb family. 5225-5234
  
• E. Pays, M. F. Delauw, M. Laurent, M. Steinert:
  Possible DNA modification in GC dinucleotides of Trypanosoma brucei telomeric sequences; relationship with antigen gene transcription. 5235-5247
  
• H. R. Jaenichen, M. Pech, W. Lindenmaier, N. Wildgruber, H. G. Zachau:
  Composite human VK genes and a model of their evolution. 5249-5263
  
• B. Straubinger, M. Pech, K. Muhlebach, H. R. Jaenichen, H. G. Bauer, H. G. Zachau:
  Molecular footprints of human immunoglobulin gene evolution: a new sequence family. 5265-5275
  
• D. A. Hartley, K. E. Davies, D. Drayna, R. L. White, R. Williamson:
  A cytological map of the human X chromosome - evidence for non-random recombination. 5277-5285
  
• S. H. Shanblatt, A. Revzin:
  Kinetics of RNA polymerase-promoter complex formation: effects of nonspecific DNA-protein interactions. 5287-5306
  
• K. Ohmura, K. Nakamura, H. Yamazaki, T. Shiroza, Kunio Yamane, Y. Jigami, H. Tanaka, K. Yoda, M. Yamasaki, G. Tamura:
  Length and structural effect of signal peptides derived from Bacillus subtilis alpha-amylase on secretion of Escherichia coli beta-lactamase in B. subtilis cells. 5307-5319
  
• A. Spassky, S. Rimsky, H. Garreau, H. Buc:
  H1a, an E. coli DNA-binding protein which accumulates in stationary phase, strongly compacts DNA in vitro. 5321-5340
  
• S. Sharma, T. Stark, R. E. Moses:
  Distal regulatory functions for the uvrC gene of E. coli. 5341-5354
  
• N. Murphy, D. J. McConnell, B. A. Cantwell:
  The DNA sequence of the gene and genetic control sites for the excreted B. subtilis enzyme beta-glucanase. 5355-5367
  
• J. B. Watson, D. W. Chandler, J. D. Gralla:
  Specific termination of in vitro transcription by calf thymus RNA polymerase III. 5369-5384
  
• T. I. Serenkova, A. M. Mazo, T. D. Mashkova, I. Toots, A. Nigul, M. Ya Timofeeva, L. L. Kisselev:
  The secondary structure of oocyte and somatic 5S ribosomal RNAs of the fish Misgurnus fossilis L. from nuclease hydrolyses and chemical modification data. 5385-5404
  
• P. Loidl, A. Loidl, B. Puschendorf, P. Grobner:
  RNA polymerase activity and template activity of chromatin after butyrate induced hyperacetylation of histones in Physarum. 5405-5417
  
• P. P. Lankhorst, C. A. Haasnoot, C. Erkelens, Cornelis Altona:
  Carbon-13 NMR in conformational analysis of nucleic acid fragments. 3. The magnitude of torsional angle epsilon in d(TpA) from CCOP and HCOP NMR coupling constants. 5419-5428
  
• S. Boiteux, J. Belleney, Bernard-Pierre Roques, J. Laval:
  Two rotameric forms of open ring 7-methylguanine are present in alkylated polynucleotides. 5429-5439
  
• F. Takaiwa, K. Oono, Masahiro Sugiura:
  The complete nucleotide sequence of a rice 17S rRNA gene. 5441-5448
  
• X. M. Yu, W. S. Reznikoff:
  Deletion analysis of the CAP-cAMP binding site of the Escherichia coli lactose promoter. 5449-5464
  
• B. A. Morgan, E. Kellett, R. S. Hayward:
  The wild-type nucleotide sequence of the rpoBC-attenuator region of Escherichia coli DNA and its implications for the nature of the rifd18 mutation. 5465-5470
  
• M. Bishop, E. Thompson:
  Fast computer search for similar DNA sequences. 5471-5474
  
• Rick P. Millane, J. K. Walker, S. Arnott, R. Chandrasekaran, D. L. Birdsall, R. L. Ratliff:
  Structure of a pleiomeric form of poly d(AT): poly d(AT). 5475-5493
  
• P. O. O'Connell, M. Rosbash:
  Sequence, structure, and codon preference of the Drosophila ribosomal protein 49 gene. 5495-5513
  
• P. Perrin:
  Coding strategy differences between constant and variable segments of immunoglobulin genes. 5515-5527
  
• Jens G. Reich, H. Drabsch, A. Daumler:
  On the statistical assessment of similarities in DNA sequences. 5529-5543
  

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