Home LiteratureArticle Details
PMID: 3003673 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

A comprehensive package for DNA sequence analysis in FORTRAN IV for the PDP-11.

Nucleic acids research ·Vol. 14 ·No. 1 ·1986-01-10 ·Pages 239-54

Arnold J, Eckenrode VK, Lemke K, Phillips GJ, Schaeffer SW

Abstract

A computer package written in Fortran-IV for the PDP-11 minicomputer is described. The package's novel features are: software for voice-entry of sequence data; a less memory intensive algorithm for optimal sequence alignment; and programs that fit statistical models to nucleic acid and protein sequences.

MeSH Terms
Base Sequence Computers DNA/analysis DNA Restriction Enzymes/metabolism Escherichia coli/genetics Mathematics Minicomputers Models, Genetic Proteins/analysis,genetics Software
Chemicals
Proteins DNA DNA Restriction Enzymes
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Arnold J
Eckenrode V K
Lemke K
Phillips G J
Schaeffer S W
References (37)
37 references, click to expand
  1. The universal dinucleotide asymmetry rules in DNA and the amino acid codon choice.
    J Mol Evol. 1981;17(4):237-44 PMID: 7021862
  2. A computer program to search for tRNA genes.
    Nucleic Acids Res. 1980 Feb 25;8(4):817-25 PMID: 7433117
  3. A large database DNA sequence handling program with generalized searching specifications.
    Nucleic Acids Res. 1982 Jan 11;10(1):115-25 PMID: 7063398
  4. Matrix program to analyze primary structure homology.
    Nucleic Acids Res. 1982 Jan 11;10(1):127-31 PMID: 6801625
  5. Pattern recognition in nucleic acid sequences. I. A general method for finding local homologies and symmetries.
    Nucleic Acids Res. 1982 Jan 11;10(1):247-63 PMID: 6801626
  6. MAXAMIZE. A DNA sequencing strategy advisor.
    Nucleic Acids Res. 1982 Jan 11;10(1):295-304 PMID: 6278407
  7. GENESIS, a knowledge-based genetic engineering simulation system for representation of genetic data and experiment planning.
    Nucleic Acids Res. 1982 Jan 11;10(1):323-40 PMID: 6950365
  8. A statistical test for comparing several nucleotide sequences.
    Nucleic Acids Res. 1982 Jan 11;10(1):375-89 PMID: 7063406
  9. Electrostatic potential molecular surfaces.
    Proc Natl Acad Sci U S A. 1982 Jun;79(12):3754-8 PMID: 6285364
  10. H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences.
    J Biol Chem. 1983 Jan 25;258(2):1318-27 PMID: 6822501
  11. Contextual constraints on synonymous codon choice.
    J Mol Biol. 1983 Jan 25;163(3):363-76 PMID: 6834430
  12. Intelligent computational assistance for experiment design.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):11-29 PMID: 6320088
  13. Fast optimal alignment.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):175-9 PMID: 6694900
  14. On the statistical significance of nucleic acid similarities.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):215-26 PMID: 6694902
  15. Computer programs for handling nucleic acid sequences.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):379-86 PMID: 6546422
  16. A comprehensive set of sequence analysis programs for the VAX.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387-95 PMID: 6546423
  17. Computer-based image analysis of one-dimensional electrophoretic gels used for the separation of DNA restriction fragments.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):473-91 PMID: 6320097
  18. A computer program to enter DNA gel reading data into a computer.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):499-503 PMID: 6546430
  19. Graphic methods to determine the function of nucleic acid sequences.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):521-38 PMID: 6364040
  20. Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):551-67 PMID: 6364041
  21. An inexpensive semi-automated sequence reader for the Apple II computer.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):675-8 PMID: 6198628
  22. DNAGEL: a computer program for determining DNA fragment sizes using a small computer equipped with a graphics tablet.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):679-88 PMID: 6320102
  23. Transcription of the uvrD gene of Escherichia coli is controlled by the lexA repressor and by attenuation.
    Nucleic Acids Res. 1983 Dec 20;11(24):8625-40 PMID: 6324092
  24. Comparison of the nucleotide sequence of soybean 18S rRNA with the sequences of other small-subunit rRNAs.
    J Mol Evol. 1984-1985;21(3):259-69 PMID: 6100313
  25. A prevalent persistent global nonrandomness that distinguishes coding and non-coding eucaryotic nuclear DNA sequences.
    J Mol Evol. 1983;19(2):122-33 PMID: 6571217
  26. Codon preference and its use in identifying protein coding regions in long DNA sequences.
    Nucleic Acids Res. 1982 Jan 11;10(1):141-56 PMID: 7063399
  27. A general method applicable to the search for similarities in the amino acid sequence of two proteins.
    J Mol Biol. 1970 Mar;48(3):443-53 PMID: 5420325
  28. A test for nucleotide sequence homology.
    J Mol Biol. 1973 Jun 15;77(1):169-64 PMID: 4203659
  29. A new method for sequencing DNA.
    Proc Natl Acad Sci U S A. 1977 Feb;74(2):560-4 PMID: 265521
  30. Sequence data handling by computer.
    Nucleic Acids Res. 1977 Nov;4(11):4037-51 PMID: 593900
  31. DNA sequencing with chain-terminating inhibitors.
    Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7 PMID: 271968
  32. Further procedures for sequence analysis by computer.
    Nucleic Acids Res. 1978 Mar;5(3):1013-6 PMID: 643613
  33. A method for detecting distant evolutionary relationships between protein or nucleic acid sequences in the presence of deletions or insertions.
    J Mol Evol. 1978 Jun 20;11(2):143-61 PMID: 671562
  34. Computer programs for the assembly of DNA sequences.
    Nucleic Acids Res. 1979 Sep 25;7(2):529-45 PMID: 493154
  35. Computer analysis of nucleic acids and proteins.
    Methods Enzymol. 1980;65(1):595-609 PMID: 6154871
  36. Steps toward computer analysis of nucleotide sequences.
    Science. 1980 Sep 19;209(4463):1322-8 PMID: 6251542
  37. A semi-automated method for the reading of nucleic acid sequencing gels.
    Nucleic Acids Res. 1982 Jan 11;10(1):103-14 PMID: 7063397
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/14.1.239
Published
1986-01-10
Pages
239-54
Language
English
Region
England
NLM ID
0411011
PMCID
PMC339390
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/14.1.239 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2