• References
  • Altschul, S. F., Gish, W., Miller, W., Myers, E.W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215: 403.

    Bairoch, A. and Apweiler, R. (1996). The SWISS-PROT Protein Sequence Data Bank and Its New Supplement. TREMBL. Nucleic Acids Res. 24: 21.

    Bairoch, A., Bucher, P., and Hofmann, K. (1996). The PROSITE Database, Its Status in 1995. Nucleic Acids Res. 24: 189.

    Benson, D.A., Boguski, M.S., Lipman, D.J., and Ostell, J. (1996). GenBank. Nucleic Acids Res. 24: 1.

    Bolton, E.T. and McCarthy, B.J. (1962) A General Method for the Isolation of RNA Complementary to DNA. Proc. Natl. Acad. Sci. 48:1390.

    Casey, J. and Davidson, N. (1977) Rates of Formation and Thermal Stabilities of RNA:DNA and DNA:DNA Duplexes at High Concentrations of Formamide. Nucleic Acids Res. 4:1539.

    Eisenberg, D., Sweet, R.M., and Terwilliger, T.C. (1984). The Hydrophobic Moment Detects Periodicity in Protein Hydrophobicity. Proc. Natl. Acad. Sci. 81: 140.

    Feng, D.F. and Doolittle, R.F (1987). Progressive Sequence Alignment as a Prerequisite to Correct Phylogenetic Trees. J. Mol. Evol. 25: 351.

    Garnier, J., Osguthorpe, D.J., and Robson, B. (1978). Analysis of the Accuracy and Implications of Simple Methods for Predicting the Secondary Structure of Globular Proteins. J. Mol. Biol. 120: 97.

    Grantham, R., Gautier, C., Guoy, M., Jacobzone, M., and Mercier R. (1981). Codon Catalog Usage Is a Genome Strategy Modulated for Gene Expressivity. Nucleic Acids Res. 9: r43.

    Gribskov, M. and Burgess, R.R. (1986) Sigma factors from E. coli, B. subtilis, phage SP01, and phage T4 are homologous proteins. Nucleic Acids Res. 14: 6745.

    Gribskov, M., Devereux, J., and Burgess, R.R. (1984). The Codon Preference Plot: Graphic Analysis of Protein Coding Sequences and Prediction of Gene Expression. Nucleic Acids Res. 12: 539.

    Henikoff, Steven and Henikoff, Jorga G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. 89: 10915.

    Higgins, D.G. and Sharp, P.M. (1988). CLUSTAL: A Package for Performing Multiple Sequence Alignment on a Microcomputer. Gene 73: 237.

    Higgins, D.G. and Sharp, P.M (1989). Fast and Sensitive Multiple Sequence Alignments on a Microcomputer. Computer Applications in the Biosciences 5: 151.

    Hopp, T.P. and Woods K.R. (1981) Prediction of Protein Antigenic Determinants from Amino Acid Sequences. Proc. Natl. Acad. Sci. 78:3824.

    Huang, Y. and Zhang, L. (2004) Rapid and Sensitive dot-matrix methods for geneome analysis. Bioinformatics 20:460.

    Ikuta, S., Takagi, K., Wallace, R.B. and Itakura, K. (1987). Dissociation Kinetics of 19 Base Paired Oligonucleotide-DNA Duplexes Containing Different Single Mismatched Base Pairs. Nucleic Acids Res. 15:797.

    King, R.D. and Sternberg, M.J.E. (1996) Identification and Application of the Concepts Important for Accurate and reliable Protein Secondary Structure Prediction . Protein Science 5:2298

    Kyte, J. and Doolittle, R.F. (1982). A Simple Method for Displaying the Hydropathic Character of a Protein. J. Mol. Biol. 157: 105.

    Lipman, D.J. and Pearson, W.R. (1985). Rapid and Sensitive Protein Similarity Searches. Science 227: 1435.

    Maizel, J.V. and Lenk, R.P. (1981). Enhanced Graphic Matrix Analysis of Nucleic Acid and Protein Sequences. Proc. Natl. Acad. Sci. 78: 7665.

    Maniatis, T., Fritsch, E.F. and Sambrook. (1988) Molecular Cloning: a Laboratory Manual. Clod Spring Harbor Laboratory. Cold Spring Harbor, N.Y. Page: 9.51 and 11.46.

    McClelland, M. and Nelson, M. (1988) The Effect of Site-Specific DNA Methylation on Restriction Endonucleases and DNA Modification Methyltransferases - a View. Gene 74:291.

    Needleman, S.B. and Wunsch, C.D. (1970). A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins. J. Mol. Biol. 48: 443.

    Pearson, W.R. and Lipman, D.J. (1988). Improved Tools for Biological Sequence Analysis. Proc. Natl. Acad. Sci. 85: 2444.

    Pearson, W.R. (1990). Rapid and Sensitive Sequence Comparison with FASTP and FASTA. In Methods in Enzymology , (R.F. Doolittle, ed.), 183, 63-98, Academic Press, San Diego, California, USA.

    Pearson, W.R. (1995). Comparison of Methods for Searching Protein Sequence Databases. Protein Science 4: 1145.

    Roberts, R.J. and Macelis, D. (1996). REBASE - Restriction Enzymes and Methylases. Nucleic Acids Res. 24: 223.

    Rodriguez-Tome, P., Stoehr, P.J., Cameron, G.N., and Flores, T.P. (1996). The European Bioinformatics Institute (EBI) Databases. Nucleic Acids Res. 24: 6.

    Rychlik, W. and Rhoads, R.E. (1990). Optimization of the Annealing Temperature for DNA Amplification in virtro. Nucleic Acids Res. 18: 6409.

    Saitou, N. and Nei, M. (1987). The Neighbor-joining Method: A New Method for Reconstructing Phylogenetic Trees. Mol. Biol. Evol. 4: 406.

    Schwartz, R.M. and Dayhoff, M.O. (1979). Matrices for Detecting Distant Relationships. In Atlas of Protein Sequences and Structure , (M.O. Dayhoff, ed.), 5, Suppl. 3, 353-358, National Biomedical Research Foundation, Washington, D.C., USA.

    Smith, T.F. and Waterman, M.S. (1981). Comparison of Bio-Sequences. Advances in Applied Mathematics 2: 482.

    Smith, T.F., Waterman, M.S., and Sadler, J.R. (1983). Statistical Characterization of Nucleic Acid Sequence Functional Domains. Nucleic Acids Res. 11: 2205.

    Gill, S.C. and von Hippel P. H. (1989). Calculation of Protein Extinction Coefficients from Amino Acid Sequence Data. Analytical Biochemistry. 182: 319.

    Studier, J.A. and Keppler, K.J. (1988). A Note on the Neighbor-joining Algorithm of Saitou and Nei. Mol. Biol. Evol. 5: 729.

    Tajima, F. and Nei, M. (1984). Estimation of Evolutionary Distance between Nucleotide Sequences. Mol. Biol. Evol. 1: 269.

    Thompson, J.D., Higgins, D.G., and Gibson T.J. (1994). CLUSTALW: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting Position-Specific Gab Penalties and Weight Matrix Choice. Nucleic Acids Res. 22:4673.

    Wilbur, W.J. and Lipman, D.J. (1983). Rapid Similarity Searches of Nucleic Acid and Protein Data Banks. Proc. Natl. Acad. Sci. 80: 726.

    Wilbur, W.J. and Lipman, D.J. (1984). The Context Dependent Comparison of Biological Sequences. SIAM J. Appl. Math. 44: 557.