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REFERENCES
Note: OCR errors may be found in this Reference List extracted from the full text article. ACM has opted to expose the complete List rather than only correct and linked references.
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AGM+90
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S.F. Altshul, W. Gish, W. Miller, Myers E. W., and Lipman D. J. Basic local alignment search tool. J. Mol. Biol., 215, 1990.
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AHO93
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K. Asai, S. Hayamizu, and K. Onizuka. HMM with protein structure grammar. In Proceedings r~'the Hawaii International Conference on System Sciences, pages 783-791, Los Alamitos, CA, 1993. IEEE Computer Society Press.
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B.96
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Hazes B. The (qxw)3 domain: A flexible lectin scaffold. Protein Science, 5(8): 1490-1501, August 1996.
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Bat96
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A. Bateman. Fibronectin type iii domains ill yeast detected by a hidden markov model. Current Biology, 6( 12): 1544-1547, December 1996.
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Bat97
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A. Bateman. The structure of a domain common to archaebacteria and the homocystinuria disease protein. Trends in Biochemical Sciences, 22( 1 ): 12-13, January i 997.
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BB94
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Philipp Bucher and Amos Bairoch. A generalized prolile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation. In ISMB-94, pages 53- 6 I, Menlo Park, CA, 1994. AAAI/MIT Press.
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BCHM94
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R Baldi, Y. Chauvin, T Hunkapillar, and M. McClure. Hidden Markov models of biological primary sequence information. PNAS, 91:1059-1063, 1994.
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BE95
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Timothy L. Bailey and Charles Elkan. The value of prior knowledge in discovering motifs with MEME. In ISMB-95, pages 21-29, Menlo Park, CA, July 1995. AAAI/MIT Press.
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BEC96
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A. Bateman, S. Eddy, and C. Chothia. Members of the immunoglobulin superfamily in bacteria. Protein Science, 5:1939-194 I, 1996.
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BG96
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M. Burset and R. Guigo. Evaluation of gene structure prediction programs. Genomics, 34(3):353-367, 1996. Data set and evaluation results can be found at http://www.imim.es/GeneldentificationfEvaluation/Index.html.
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BHK+93
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Michael Brown , Richard Hughey , Anders Krogh , I. Saira Mian , Kimmen Sjölander , David Haussler, Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families, Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology, p.47-55, July 01, 1993
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BK97
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C. Burge and S. Karlin. Prediction of complete gene structure in genomic DNA. JMB, 1997. In press.
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BLE91
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J.U. Bowie, R. L0thy, and D. Eisenherg. A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253:164-170, 1991.
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BM93
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M. Borodovsky and J. Mclninch. Genmark: Parallel gene recognition for both DNA strands. Computers and Chemistr3,, 17(2):123-133, 1993.
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BS90
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G.J. Barton and M. J. Sternherg. Flexible protein sequence patterns: A sensitive method to detect weak structural similarities. JMB, 212(2):389-402, 1990.
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Cho92
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C. Chothia. One thousand families for the molecular biologist. Nature, 357:543-544, 1992.
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CS92
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L.R. Cardon and G. D. Stormo. Expectation maximization algorithm for identifying proteinbinding sites with variable lengths from unaligned DNA fragments. JMB. 223:159-170, 1992.
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DMHM97
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J. Dalgaard, M Moser, R. Hughey, and S. Mian. Statistical modeling, phylogenetic analysis and structure prediction of a protein splicing domain common to inteins and hedgehog proteins. manuscript, 1997.
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DS94
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S. Dong and D. B. Searls. Gene structure prediction by linguistic methods. Genomics, 162:705-708, 1994.
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ED94
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S.R. Eddy and R. Durbin. RNA sequence analysis using covariance models. NAR, 22:2079- 2088, 1994.
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Edd95
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Sean Eddy. Multiple alignment using hidden Markov models. In Christopher Railings et al., editors, ISMB-95, pages 114-120, Menlo Park, CA, July 1995. AAAI/M1T Press.
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Edd96
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S.R. Eddy. Hidden markov models. Curr. Opin. Struct. Biol., 1996.
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EMD95
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S.R. Eddy, G. Mitchison, and R. Durbin. Maximum discrimination hidden Markov models of sequence consensus. J. Comput. Biol., 2:9-23, 1995.
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Fic96a
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J.W. Fickett. Finding genes by computer - the state of the art. Trends in Genetics, 12(8):316- 320, 1996.
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Fic96b
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J.W. Fickett. The gene identification problem - an overview for developers. Computers and Chemistry, 20(1): 103-118, 1996.
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Gel95
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M.S. Gelfand. Prediction of function in dna sequence analysis. Jour. Comp. Biol., 2(1):87- 115, 1995.
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GLE90
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M. Gribskov, R. L/ithy, and D. Eisenberg. Profile analysis. Methods in Enzymology, 183:146- 159, 1990.
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GMP96
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M.S. Gelfand, A. A. Mironov, and P. A. Pevzner. Gene recognition via spliced sequence alignment. PNAS, 93(17):9061-9066, 1996.
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HH91
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Steven Henikoff and Jorja G. Henikoff. Automated assembly of protein blocks for database searching. NAR, 19(23):6565-6572, 1991.
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HH96
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Jorja G. Henikoff and Steven Henikoff. Using substitution probabilities to improve positionspecific scoring matrices. CABIOS, 12(2): 135- 143, 1996.
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HK95
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HWB90
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Steven Henikoff, James C. Wallace, and Joseph P. Brown. Finding protein similarities with nucleofide sequence databases. Methods Enzymol., 183:111-132, 1990.
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KBM+94
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A. Krogh, M. Brown, I. S. Mian, K. Sj61ander, and D. Haussler. Hidden Markov models in computational biology: Applications to protein modeling. JMB, 235:150 !-1531, February 1994.
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KHRE96
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KMH94
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A. Krogh, I. S. Mian, and D. Haussler. A Hidden Markov Model that finds genes in E. coli DNA. NAR, 22:4768-4778, 1994.
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LAB +93
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C.E. Lawrence, S. Altschul, M. Boguski, J. Liu, A. Neuwald, and J. Wootton. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science, 262:208-214, 1993.
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LME91
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R. Liithy, A. D. McLachlan, and D. Eisenberg. Secondary structure-based profiles: Use of structure-conserving scoring table in searching protein sequence databases for structural similarities. Proteins: Structure, Function, and Genetics, 10:229-239, 1991.
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LR90
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C.E. Lawrence and A. A. Reilly. An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins, 7:41-51, 1990.
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NJD96
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Goldman N., Thorne J.L., and Jones D.T Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. JMB, 263(2):196-208, October 25 1996.
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Pea90
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W.R. Pearson. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol., 183:63-98, 1990.
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Pen96
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Elizabeth Pennisi. Teams tackle protein prediction. Science, 273:426-428, 26 July 1996.
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Rab89
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Lawrence R. Rabiner. A tutorial on hidden Markov models and selected applications in speech recognition. Proc. of the IEEE, 77(2):257-286, February 1989.
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SAL94
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V. Soiovyev, Salamov A., and C. Lawrence. Predicting internal exons by oligonucleotide composition and discriminant analysis of splicable open reading frames. Nucl. Acids Res., 22:5156-5163, 1994.
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SBH+94
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Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen SjiSlander, Rebecca C. Underwood, and David Haussler. Stochastic context-free grammars for tRNA modeling. NAR, 22:5112-5120, 1994.
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SKB+96
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K. Sj61ander, K. Karplus, M. P. Brown, R. Hughey, A. Krogh, I. S. Mian, and D. Haussler. Dirichlet mixtures: A method for improving detection of weak but significant protein sequence homology. CABIOS, 12(4):327-345, 1996.
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SS95
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E. Snyder and G. Stormo. Indentification of protein coding regions in genomic dna. JMB, 248, 1995.
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SWS93
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C.M. Stultz, J. V. White, and T. F. Smith. Structural analysis based on state-space modeling. Protein Science, 2:305-315, 1993.
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TAK94
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Roman L. Tatusov, Stephen E Altschul, and Eugen V. Koonin. Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks. PNAS, 91:12091-12095, December 1994.
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Tau96
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Gary Taubes. Software matchmakers help make sense of sequences. Science, 273:588-590, 2 August 1996.
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THG94
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Julie D. Thompson, Desmond G. Higgins, and Toby J. Gibson. Improved sensitivity of profile searches through the use of sequence weights and gap excision. CABIOS, 10(1 ): 19-29, 1994.
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WMS+96
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Jason T L. Wang, Thomas G. Mart, Dennis Shasha, Bruce Shapiro, Gung-Wei Chirn, and T. Y. Lee. Complementary classification approaches for protein sequences. Protein Engr., to appear 1996.
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WP86
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M.S. Waterman and M. D. Periwitz. Line geometries for sequence comparisons. Bull. Math. Biol., 46:567-577, 1986.
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XESU94
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Y. Xu, J. R. Einstein, M. Shah, and E. C. Uberbacher. An improved system for exon recognition and gene modeling in human dna sequences. In ISMB-94, Menlo Park, CA, 1994. AAAI/MIT Press.
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