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Proc Natl Acad Sci U S A. Dec 1981; 78(12): 7665–7669.
PMCID: PMC349330

Enhanced graphic matrix analysis of nucleic acid and protein sequences.

Abstract

The enhanced graphic matrix procedure analyzes nucleic acid and amino acid sequences for features of possible biological interest and reveals the spatial patterns of such features. When a sequence is compared to itself the technique shows regions of self-complementarity, direct repeats, and palindromic subsequences. Comparison of two different sequences, exemplified by immunoglobulin kappa light chain genes, by using colored graphic matrices showed domains of similarity, regions of divergence, and features explainable by transpositions. Analysis of mouse constant domain immunoglobulin sequences revealed self-complementary regions that can be used to fold the molecule into a structure consistent with electron microscopic observations. Computer translation of nucleic acid sequences into all possible amino acid sequences followed by graphic matrix analysis provides a way to detect the most likely protein encoding regions and can predict the correct reading frames in sequences in which splicing patterns are not defined. Application of this technique to regions of simian virus 40 and polyoma virus demonstrates the frames of translation and shows the agreement of sequences determined in separate laboratories with different virus isolates. The graphic matrix technique can also be used to assemble fragmentary sequences during determination, to display local variations in base composition, to detect distant evolutionary relationships, and to display intragenic variation in rates of evolution.

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Selected References

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  • Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. [PMC free article] [PubMed]
  • Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. [PMC free article] [PubMed]
  • Staden R. Sequence data handling by computer. Nucleic Acids Res. 1977 Nov;4(11):4037–4051. [PMC free article] [PubMed]
  • Staden R. Further procedures for sequence analysis by computer. Nucleic Acids Res. 1978 Mar;5(3):1013–1016. [PMC free article] [PubMed]
  • Staden R. A strategy of DNA sequencing employing computer programs. Nucleic Acids Res. 1979 Jun 11;6(7):2601–2610. [PMC free article] [PubMed]
  • Korn LJ, Queen CL, Wegman MN. Computer analysis of nucleic acid regulatory sequences. Proc Natl Acad Sci U S A. 1977 Oct;74(10):4401–4405. [PMC free article] [PubMed]
  • Queen CL, Korn LJ. Computer analysis of nucleic acids and proteins. Methods Enzymol. 1980;65(1):595–609. [PubMed]
  • Gingeras TR, Roberts RJ. Steps toward computer analysis of nucleotide sequences. Science. 1980 Sep 19;209(4463):1322–1328. [PubMed]
  • Tinoco I, Jr, Uhlenbeck OC, Levine MD. Estimation of secondary structure in ribonucleic acids. Nature. 1971 Apr 9;230(5293):362–367. [PubMed]
  • Gibbs AJ, McIntyre GA. The diagram, a method for comparing sequences. Its use with amino acid and nucleotide sequences. Eur J Biochem. 1970 Sep;16(1):1–11. [PubMed]
  • Fitch WM. Locating gaps in amino acid sequences to optimize the homology between two proteins. Biochem Genet. 1969 Apr;3(2):99–108. [PubMed]
  • McLachlan AD. Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c 551 . J Mol Biol. 1971 Oct 28;61(2):409–424. [PubMed]
  • Konkel DA, Maizel JV, Jr, Leder P. The evolution and sequence comparison of two recently diverged mouse chromosomal beta--globin genes. Cell. 1979 Nov;18(3):865–873. [PubMed]
  • Hieter PA, Max EE, Seidman JG, Maizel JV, Jr, Leder P. Cloned human and mouse kappa immunoglobulin constant and J region genes conserve homology in functional segments. Cell. 1980 Nov;22(1 Pt 1):197–207. [PubMed]
  • Max EE, Maizel JV, Jr, Leder P. The nucleotide sequence of a 5.5-kilobase DNA segment containing the mouse kappa immunoglobulin J and C region genes. J Biol Chem. 1981 May 25;256(10):5116–5120. [PubMed]
  • Nussinov R, Jacobson AB. Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6309–6313. [PMC free article] [PubMed]
  • Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981 Jan 10;9(1):133–148. [PMC free article] [PubMed]
  • Seidman JG, Leder A, Edgell MH, Polsky F, Tilghman SM, Tiemeier DC, Leder P. Multiple related immunoglobulin variable-region genes identified by cloning and sequence analysis. Proc Natl Acad Sci U S A. 1978 Aug;75(8):3881–3885. [PMC free article] [PubMed]
  • Nishioka Y, Leder P. Organization and complete sequence of identical embryonic and plasmacytoma kappa V-region genes. J Biol Chem. 1980 Apr 25;255(8):3691–3694. [PubMed]
  • Seidman JG, Max EE, Leder P. A kappa-immunoglobulin gene is formed by site-specific recombination without further somatic mutation. Nature. 1979 Aug 2;280(5721):370–375. [PubMed]
  • Seidman JG, Leder A, Nau M, Norman B, Leder P. Antibody diversity. Science. 1978 Oct 6;202(4363):11–17. [PubMed]
  • Hamlyn PH, Browniee GG, Cheng CC, Gait MJ, Milstein C. Complete sequence of constant and 3' noncoding regions of an immunoglobulin mRNA using the dideoxynucleotide method of RNA sequencing. Cell. 1978 Nov;15(3):1067–1075. [PubMed]
  • Reddy VB, Thimmappaya B, Dhar R, Subramanian KN, Zain BS, Pan J, Ghosh PK, Celma ML, Weissman SM. The genome of simian virus 40. Science. 1978 May 5;200(4341):494–502. [PubMed]
  • Soeda E, Arrand JR, Smolar N, Walsh JE, Griffin BE. Coding potential and regulatory signals of the polyoma virus genome. Nature. 1980 Jan 31;283(5746):445–453. [PubMed]
  • Friedmann T, Doolittle RF, Walter G. Amino acid sequence homology between polyoma and SV40 tumour antigens deduced from nucleotide sequences. Nature. 1978 Jul 20;274(5668):291–293. [PubMed]
  • Studnicka GM, Eiserling FA, Lake JA. A unique secondary folding pattern for 5S RNA corresponds to the lowest energy homologous secondary structure in 17 different prokaryotes. Nucleic Acids Res. 1981 Apr 24;9(8):1885–1904. [PMC free article] [PubMed]

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