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The information in this appendix lists the citations used throughout the set of Accelrys GCG (GCG) Package documentation.

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Altschul, S.F. (1993). A protein alignment scoring system sensitive at all evolutionary distances. Journal of Molecular Evolution36, 290-300.

Altschul, S.F., Boguski, M.S., Gish, W., and Wootton, J.C. (1994). Issues in searching molecular sequence databases. Nature Genetics 6, 119-129.

Altschul, S.F. and Erickson, B.W. (1985). Significance of nucleotide sequence alignments: A method for random sequence permutation that preserves dinucleotide and codon usage. Molecular Biology and Evolution 2, 526-538.

Altschul, S.F., and Gish, Warren. (1996). Local Alignment Statistics. In Methods in Enzymology, (R. Doolittle, ed.), 266, 460-480, Academic Press, San Diego, California, USA.

Altschul, Stephen F., Gish, Warren, Miller, Webb, Myers, Eugene W., and Lipman, David J. (1990). Basic local alignment search tool. Journal of Molecular Biology 215, 403-410.

Altschul, Stephen F., Madden, Thomas L., Schaffer, Alejandro A., Zhang, Jinghui, Zhang, Zheng, Miller, Webb, and Lipman, David J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25(17), 3389-3402.

Bailey, T.L. and Elkan, C. (1994). Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, California, USA, 28-36.

Bailey, T.L. and Gribskov, M. (1998). Combining evidence using p-values: application application to sequence homology searches. Bioinformatics, 14(1), 48-54.

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Borer, P.N., Dengler, B., and Tinoco, I., Jr. (1974). Stability of Ribonucleic Acid and Double-stranded Helices. Journal of Molecular Biology 86, 843-853.

Brendel, V. and Trifonov, E.N. (1984). A Computer Algorithm for Testing Prokaryotic Terminators. Nucleic Acids Research12, 4411-4427.

Brendel, V. and Trifonov, E.N. (1984). CODATA Conference Proceedings, Jerusalem.

Breslauer, K.J., Frank, R., Blocker, H., and Marky, L.A. (1986). Predicting DNA Duplex Stability from the Base Sequence. Proceedings of the National Academy of Sciences USA 83, 3746-3750.

Chao, K.M., Pearson, W.R. and Miller, W. (1992). Aligning Two Sequences within a Specified Diagonal Band. Computer Applications in the Biosciences 8(5), 481-487.

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Claverie, J.-M. and Audic, S. (1996). The statistical significance of nucleotide position-weight matrix matches. CABIOS 12(5), 431-439.

Claverie, J.-M. and States, D.J. (1993). Information enhancement methods for large-scale sequence analysis. Computers and Chemistry 17, 191-201.

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Eddy, S.R. (1996). Hidden Markov Models. Current Opinion in Structural Biology 6, 361-365.

Eddy, S.R. (1998). Profile hidden Markov models. Bioinformatics, 14, 755-763.

Eisenberg, D., Sweet, R.M., and Terwilliger, T.C. (1984). The Hydrophobic Moment Detects Periodicity in Protein Hydrophobicity. Proceedings of the National Academy of Sciences USA 81, 140-144.

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Engelman, D.M., Steitz, T.A., and Goldman, A. (1986). Identifying Nonpolar Transbilayer Helices in Amino Acid Sequences of Membrane Proteins. Annual Review of Biophysics and Biophysical Chemistry 15, 321-353.

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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 Research 12, 539-549.

Gribskov, M., McLachlan, M., and Eisenberg, D. (1987). Profile Analysis: Detection of Distantly Related Proteins. Proceedings of the National Academy of Sciences USA 84, 4355-4358.

Gribskov, M., Homyak, M., Edenfield, J., and Eisenberg, D. (1988). Profile Scanning for Three-Dimensional Structural Patterns in Protein Sequences. Computer Applications in the Biosciences 4, 61-66.

Gribskov, M. and Eisenberg, D. (1989). Detection of Protein Structural Features With Profile Analysis. In Techniques in Protein Chemistry, (T.E. Hugli, ed.), Academic Press, San Diego, California, USA, 108-117.

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Higgins, D.G. and Sharp, P.M. (1988). CLUSTAL: A Package for Performing Multiple Sequence Alignment on a Microcomputer. Gene 73, 237-244.

Higgins, D.G. and Sharp, P.M (1989). Fast and Sensitive Multiple Sequence Alignments on a Microcomputer. Computer Applications in the Biosciences 5, 151-153.

Hillier, L. and Green, P. (1991). OSP: A Computer Program for Choosing PCR and DNA Sequencing Primers. PCR Methods and Applications 1, 124-128.

Hogeweg, P. and Hesper, B. (1984). Energy Directed Folding of RNA Sequences. Nucleic Acids Research 12, 67-74.

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Jaeger, J.A., Turner, D.H., and Zuker, M. (1989). Improved Predictions of Secondary Structures for RNA. Proceedings of the National Academy of Sciences USA 86, 7706-7710.

Jaeger, J.A., Turner, D.H., and Zuker, M. (1990). Predicting Optimal and Suboptimal Secondary Structures for RNA. In Methods in Enzymology, (R.F. Doolittle, ed.), 183, 281-306, Academic Press, San Diego, California, USA.

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Karlin, S. and Altschul, S.F. (1990). Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proceedings of the National Academy of Sciences USA 87, 2264-2268.

Karlin, S. and Altschul, S.F. (1993). Applications and statistics for multiple high-scoring segments in molecular sequences. Proceedings of the National Academy of Sciences USA 90, 5873-5877.

Karplus, P.A. and Schulz, G.E. (1985). Prediction of Chain Flexibility in Proteins. Naturwissenschaften 72, 212-213.

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Kimura, M. (1980). A Simple Method for Estimating Evolutionary Rates of Base Substitutions Through Comparative Studies of Nucleotide Sequences. Journal of Molecular Evolution 16, 111-120.

Kimura, M. (1983). The Neutral Theory of Molecular Evolution, Cambridge University Press, Cambridge, UK.

Kyte, J. and Doolittle, R.F. (1982). A Simple Method for Displaying the Hydropathic Character of a Protein. Journal of Molecular Biology 157, 105-132.

Li, Wen-Hsiung (1993). Unbiased Estimation of the Rates of Synonymous and Nonsynonymous Substitution. Journal of Molecular Evolution 36, 96-99.

Lipman, D.J. and Pearson, W.R. (1985). Rapid and Sensitive Protein Similarity Searches. Science 227, 1435-1441.

Lupas, A. (1996). Prediction and Analysis of Coiled-Coil Structures. In Methods in Enzymology, (R.F. Doolittle, ed.), 266, 513-525, Academic Press, San Diego, California, USA.

Lupas, A., Van Dyke, M., and Stock, J. (1991). Predicting Coiled Coils from Protein Sequences. Science 252, 1162-1164.

Maddison, D.R., Swofford, D.W., and Maddison, W.P. (1997). NEXUS: an extensible file format for systematic information. Systematic Biology 46, 590-621.

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Moller, S., Croning, M.D.R., and Apweiler, R. (2001). Evaluation of Methods for the prediction of membrane spanning regions. Bioinformatics, 17(7), 646-653.

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Osterburg, G. and Sommer, R. (1981). Computer Support of DNA Sequence Analysis. Computer Programs in Biomedicine13, 101-109.

Pamilo, P, and Bianchi, N.O. (1993). Evolution of the Zfx and Zfy Genes: Rates and Interdependence between the Genes. Molecular Biology and Evolution 10, 271-281.

Pearson, W.R. and Lipman, D.J. (1988). Improved Tools for Biological Sequence Analysis. Proceedings of the National Academy of Sciences USA85, 2444-2448.

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, 1145-1160.

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