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. 1982 May 11;10(9):2951–2961. doi: 10.1093/nar/10.9.2951

An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences.

R Staden
PMCID: PMC320667  PMID: 7099970

Abstract

This paper describes a computer program designed to look for similarities between pairs of nucleic or amino acid sequences. The program looks both for segments of perfect identity or for regions where, using a scoring matrix, a minimum value is exceeded. The results of comparisons are presented as a matrix which is displayed on a simple graphics terminal. Use of a graphics terminal allows the user to display the whole of the two sequences in one screenful or to home-in on regions of interest to examine them in more detail. The program is interactive and so the user can easily see the effect of changes to variables and can use inbuilt editing functions to make insertions to produce alignments of the two sequences. These aligned sequences can then be saved on disk files for further processing.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Fitch W. M. Locating gaps in amino acid sequences to optimize the homology between two proteins. Biochem Genet. 1969 Apr;3(2):99–108. doi: 10.1007/BF00520346. [DOI] [PubMed] [Google Scholar]
  2. Gibbs A. J., McIntyre G. A. The diagram, a method for comparing sequences. Its use with amino acid and nucleotide sequences. Eur J Biochem. 1970 Sep;16(1):1–11. doi: 10.1111/j.1432-1033.1970.tb01046.x. [DOI] [PubMed] [Google Scholar]
  3. Goad W. B., Kanehisa M. I. Pattern recognition in nucleic acid sequences. I. A general method for finding local homologies and symmetries. Nucleic Acids Res. 1982 Jan 11;10(1):247–263. doi: 10.1093/nar/10.1.247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Harr R., Hagblom P., Gustafsson P. Two-dimensional graphic analysis of DNA sequence homologies. Nucleic Acids Res. 1982 Jan 11;10(1):365–374. doi: 10.1093/nar/10.1.365. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Jagadeeswaran P., McGuire P. M., Jr Interactive computer programs in sequence data analysis. Nucleic Acids Res. 1982 Jan 11;10(1):433–447. doi: 10.1093/nar/10.1.433. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Kanehisa M. I. Los Alamos sequence analysis package for nucleic acids and proteins. Nucleic Acids Res. 1982 Jan 11;10(1):183–196. doi: 10.1093/nar/10.1.183. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Korn L. J., Queen C. L., Wegman M. N. Computer analysis of nucleic acid regulatory sequences. Proc Natl Acad Sci U S A. 1977 Oct;74(10):4401–4405. doi: 10.1073/pnas.74.10.4401. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. MacLeod A. R., Karn J., Brenner S. Molecular analysis of the unc-54 myosin heavy-chain gene of Caenorhabditis elegans. Nature. 1981 Jun 4;291(5814):386–390. doi: 10.1038/291386a0. [DOI] [PubMed] [Google Scholar]
  9. Maizel J. V., Jr, Lenk R. P. Enhanced graphic matrix analysis of nucleic acid and protein sequences. Proc Natl Acad Sci U S A. 1981 Dec;78(12):7665–7669. doi: 10.1073/pnas.78.12.7665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. McLachlan A. D. Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c 551 . J Mol Biol. 1971 Oct 28;61(2):409–424. doi: 10.1016/0022-2836(71)90390-1. [DOI] [PubMed] [Google Scholar]
  11. Needleman S. B., Wunsch C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970 Mar;48(3):443–453. doi: 10.1016/0022-2836(70)90057-4. [DOI] [PubMed] [Google Scholar]
  12. Novotny J. Matrix program to analyze primary structure homology. Nucleic Acids Res. 1982 Jan 11;10(1):127–131. doi: 10.1093/nar/10.1.127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Sankoff D. Matching sequences under deletion-insertion constraints. Proc Natl Acad Sci U S A. 1972 Jan;69(1):4–6. doi: 10.1073/pnas.69.1.4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Staden R. A computer program to search for tRNA genes. Nucleic Acids Res. 1980 Feb 25;8(4):817–825. [PMC free article] [PubMed] [Google Scholar]
  15. Staden R. A new computer method for the storage and manipulation of DNA gel reading data. Nucleic Acids Res. 1980 Aug 25;8(16):3673–3694. doi: 10.1093/nar/8.16.3673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Staden R. A strategy of DNA sequencing employing computer programs. Nucleic Acids Res. 1979 Jun 11;6(7):2601–2610. doi: 10.1093/nar/6.7.2601. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Staden R. Further procedures for sequence analysis by computer. Nucleic Acids Res. 1978 Mar;5(3):1013–1016. doi: 10.1093/nar/5.3.1013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Staden R., McLachlan A. D. Codon preference and its use in identifying protein coding regions in long DNA sequences. Nucleic Acids Res. 1982 Jan 11;10(1):141–156. doi: 10.1093/nar/10.1.141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Staden R. Sequence data handling by computer. Nucleic Acids Res. 1977 Nov;4(11):4037–4051. doi: 10.1093/nar/4.11.4037. [DOI] [PMC free article] [PubMed] [Google Scholar]

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