@string{AHG = "Annals of Human Genetics"}
@string{AJHG = "American Journal of Human Genetics"}
@string{ARB    = "Annual Review of Biochemistry"}
@string{ARCB   = "Annual Review of Cell Biology"}
@string{BI = "Bioinformatics"}
@string{BIOGEN = "Biochemical Genetics"}
@string{BJLS = "Biological Journal of the Linnean Society"}
@string{BMB = "Bulletin of Mathematical Biology"}
@string{CABIOS = "Computer Applications in the Biosciences"}
@string{CACM   = "Communications of the ACM"}
@string{COCB   = "Current Opinion in Cell Biology"}
@string{COSB   = "Current Opinion in Structural Biology"}
@string{CSHSQB = "Cold Spring Harbor Symposia Quantitative Biology"}
@string{ComputChem = "Computers and Chemistry"}
@string{EMBO   = "EMBO Journal"}
@string{EVO = "Evolution"}
@string{GEN = "Genetics"}
@string{JBSD   = "Journal of Biomolecular Structure and Dynamics"}
@string{JComputBiol = "Journal of Computational Biology"}
@string{JCB = JComputBiol}
@string{JMB = "Journal of Molecular Biology"}
@string{JME = "Journal of Molecular Evolution"}
@string{JRSS = "Journal of the Royal Statistical Society, B"}
@string{JTB    = "Journal of Theoretical Biology"}
@string{MBE = "Molecular Biology and Evolution"}
@string{MBIO = "Mathematical Biosciences"}
@string{ME = "Methods in Enzymology"}
@string{MPE = "Molecular Phylogenetics and Evolution"}
@string{NAR = "Nucleic Acids Research"}
@string{NC = "Neural Computation"}
@string{NNB = "Nature New Biology"}
@string{Nature = "Nature"}
@string{PE = "Protein Engineering"}
@string{PNAS = "Proceedings of the National Academy of Sciences of the USA"}
@string{PROT = "Proteins"}
@string{PROTSCI = "Protein Science"}
@string{SIAM = "SIAM Journal of Applied Mathematics"}
@string{SYSB = "Systematic Biology"}
@string{SZ = "Systematic Zoology"}
@string{Science = "Science"}
@string{S = Science}
@string{TIBTECH= "Trends in Biotechnology"}
@string{TIGS   = "Trends in Genetics"}
@string{TIBS   = "Trends in Biochemistry"}
@string{UKSB = "University of Kansas Scientific Bulletin"}


@Article{Abrahams90,
  author = 	 {J. P. Abrahams and M. van den Berg and E. van
                  Batenburg and C. Pleij},
  title = 	 {Prediction of {RNA} Secondary Structure, Including
                  Pseudoknotting, by Computer Simulation},
  journal = 	 NAR,
  year = 	 1990,
  volume =	 18,
  pages =	 {3035-3044}
}


@inproceedings{AllisonEtal92a,
  author = "L. Allison and C. S. Wallace and C. N. Yee",
  title = "Minimum message length encoding, evolutionary trees and
		  multiple alignment",
  booktitle = "Hawaii International Conference on System Sciences",
  year = "1992",
  volume = "1",
  pages = "663-674"
}

@article{AllisonEtal92b,
  author = "L. Allison and C. S. Wallace and C. N. Yee",
  title = "Finite-state models in the alignment of macromolecules.",
  journal = JME,
  year = "1992",
  volume = "35",
  pages = "77-89"
}

@techreport{AllisonWallace93,
  author = "L. Allison and C. S. Wallace",
  title = "The posterior probability distribution of alignments and its
	application to parameter estimation of evolutionary trees and to
	optimisation of muliple alignments",
  institution = "Monash University Computer Science",
  year = 1993,
  number = "TR 93/188"
}

@article{Altschul89,
  author = "S. F. Altschul",
  title = "Gap costs for multiple sequence alignment",
  journal = JTB,
  volume = 138,
  pages = "297-309",
  year = 1989
}

@Article{Altschul90,
  author = 	 "S. F. Altschul
		and W. Gish and W. Miller
		  and E. W. Myers and D. J. Lipman",
  title = 	 "Basic Local Alignment Search Tool",
  journal = 	 JMB,
  year = 	 1990,
  volume = 	 215,
  pages = 	 "403-410"
}

@Article{Altschul91,
  author = 	 "S. F. Altschul",
  title = 	 "Amino Acid Substitution Matrices from an Information
		  Theoretic Perspective",
  journal = 	 JMB,
  year = 	 1991,
  volume = 	 219,
  pages = 	 "555-565"
}

@article{AltschulErickson86,
  author = "S. F. Altschul and B. W. Erickson",
  title = "Optimal sequence alignment using affine gap costs",
  journal = BMB,
  volume = 48,
  pages = "603-616",
  year = 1986
}

@article{AltschulEtal89,
  author = "S. F. Altschul and and R. J. Carroll and D. J. Lipman",
  title = "Weights for Data Related by a Tree",
  journal = JMB,
  volume = 207,
  pages = "647-653",
  year = 1989
}

@article{SlonimEtal97,
  author = "D. Slonim and L. Kruglyak and L. Stein and E. Lander",
  title  = "Building human genome maps with radiation hybrids",
  journal = JCB,
  pages = "487-504",
  volume = 4,
  year = 1997,
}

@article{ThorneEtal96,
  author = "J. L. Thorne and N. Goldman and D. T. Jones",
  title  = "Combining protein evolution and secondary structure.",
  journal = MBE,
  volume = 13,
  pages = "666-673",
  year = 1996,
}

@article{GoldmanEtal96,
  author = "N. Goldman and J. L. Thorne and D. T. Jones",
  title  = "Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses.",
  journal = JMB,
  volume = 263,
  pages = "196-208",
  year = 1996,
}

@article{LioEtal99,
  author = "P. Lio and J. L. Thorne and N. Goldman and D. T. Jones",
  title  = "PASSML: combining evolutionary inference and protein secondary structure prediction.",
  pages  = "726-733",
  journal = BI,
  volume = 14,
  year = 1999,
}
  
@article{AltschulGish96,
author = {S. F. Altschul and W. Gish},
title = {Local alignment statistics},
journal = ME,
volume = 266,
pages = "460-480",
year = 1996
}

@Article{Altschul97,
  author = 	 {S. F. Altschul and T. L. Madden and A. A. Schaffer and
                  J. Zhang and Z. Zhang and W. Miller and D. J. Lipman},
  title = 	 {Gapped {BLAST} and {PSI-BLAST}: a New Generation of
                  Protein Database Search Programs},
  journal = 	 NAR,
  year = 	 1997,
  volume =	 25,
  pages =	 {3389-3402}
}

@Article{AltschulLipman89,
  author = 	 {S. F. Altschul and D. J. Lipman},
  title = 	 {Trees, Stars, and Multiple Biological Sequence Alignment},
  journal = 	 SIAM,
  year = 	 1989,
  volume =	 49,
  pages =	 {197-209}
}

@article{AsaiEtal93,
  author = "K. Asai and S. Hayamizu and K. Handa",
  title = "Prediction of protein secondary structure by the hidden
	{M}arkov model",
  journal = CABIOS,
  year = "1993",
  volume = "9",
  number = "2",
  pages = "141-146"
}

@book{Asmussen87,
  author = "S. Asmussen",
  title = "Applied Probability and Queues",
  publisher = "Wiley",
  address = "Chichester, UK",
  year = 1987
}

@incollection{Atteson97,
  author = "K. Atteson",
  title = "The performance of the neighbor-joining method of phylogeny reconstruction",
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  pages = "133-148",
  editor = "B. Mirkin and F. Mc{M}orris and F. Roberts and A. Rzhetsky",
  publisher = "American Mathematical Society",
  address = "Providence, RI",
  year = 1997
}

@Article{Attwood94,
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  journal = 	 PE,
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  volume =	 7,
  pages =	 {841-848}
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@inproceedings{BaileyElkan94,
  author = "T. L. Bailey and C. Elkan",
  title = "Fitting a Mixture Model by Expectation Maximization
	to Discover Motifs in Biopolymers",
  crossref = "ismb94",
  pages = "28--36"
}

@inproceedings{BaileyElkan95,
  author = "T. L. Bailey and C. Elkan",
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@inproceedings{BaileyGribskov96,
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  pages  = "15-24",
  crossref = "ismb96",
}

@inproceedings{BahlEtAl86,
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@Article{Bairoch97b,
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  volume =	 25,
  pages =	 {217-221}
}

% RD says:
% this is the correct latest swissprot reference to replace
% BairochApweiler96 in your list - I updated the only \cite{BA96} 
% in the book, in profhmm.

@Article{Bairoch97,
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@book{BaldiBrunak98,
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@article{bhattacharya99,
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@inproceedings{BaldiChauvin95,
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@article{BaldiEtal94,
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}

@article{BaldiEtal96b,
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  year = 1996
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@article{BandeltDress92,
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  year = 1992
}

@article{BartonSternberg87,
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}

@article{Barton93,
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@article{barton90,
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  year    = 1990,
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@InCollection{Baserga93,
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@article{Baum72,
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  year =         1972,
  volume =       3,
  pages =        {1-8}
}


@article{BengioEtal92,
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@book{Berger85,
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  year = 1991
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@Article{Birney93,
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@Article{Birney94,
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@Article{Birney96,
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@inproceedings{BirneyDurbin97,
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  year = 1986,
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@article{BorodovskyEtal86b,
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  year = 1986,
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  pages = "833--840"
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@article{BorodovskyEtal86c,
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  title = "Statistical Patterns in the Primary Structure of the Functional 
	Regions of the {Escherichia Coli} Genome.
	{III}. {C}omputer Recognition of Coding Regions",
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@article{BorodovskyMcIninch93,
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@Book{BoxTiao92,
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  publisher = 	 {Wiley-Interscience},
  year = 	 1992
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@Book{Branden91,
  author = 	 {C. Branden and J. Tooze},
  title = 	 {Introduction to Protein Structure},
  publisher = 	 {Garland},
  year = 	 1991,
  address =	 {New York}
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@Article{Brendel86,
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@book{Brooksetal91,
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@inproceedings{BrownEtal93,
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	K. Sj{\"o}lander and D. Haussler},
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  crossref = "ismb93"
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@Unpublished{BrownWilson95,
  author = {M. Brown and C. Wilson},
  title = {{RNA} Pseudoknot Modeling Using Intersections of
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}

@article{BrunakEtal91,
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@article{BrunakEtal90,
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@InProceedings{BucherHofmann96,
  author = 	 {P. Bucher and K. Hofmann},
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                  Probabilistic Interpretation of an Alignment Scoring System},
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  pages =	 {44-51}
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@incollection{Buneman71,
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@article{CarrilloLipman88,
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@InProceedings{CaryStormo95,
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@book{CasellaBerger90,
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  year= 1990
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@inproceedings{FujiwaraEtal94,
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% 9518021 (JID) 22202135 (UI) 

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@Article{MeyerDurbin, Author="Meyer,
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% 0404511 (JID) 22369169 (UI) 

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% 100962779 (JID) 22199598 (UI) 

@Article{Zhang2003, Author="Zhang,
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@Article{SGP2, Author="Parra,
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% 9518021 (JID) 22417273 (UI) 

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@Article{Pedersen2003, Author="Pedersen,
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% 9518021 (JID) 22505432 (UI) 

@Article{Pachter2003,
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% 0410462 (JID) 22598136 (UI) 

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Pages="859-868", Month="Apr" }

% 9518021 (JID) 20499375 (UI) 

@Article{Guigo2000, Author="Guigo, R. and Agarwal, P. and Abril, J. F. and Burset, M. and Fickett, J. W.",
Title="{An assessment of gene prediction accuracy in large DNA
sequences}", Journal="Genome Res", Year="2000", Volume="10",
Number="10", Pages="1631-1642", Month="Oct" }

