Databases:
C. Burks et al. , GenBank: Current Status and Future
Directions.
P. Kahn and G. Cameron, EMBL Data Library.
W.C. Barker, D.G. George, and L.T. Hunt, Protein Sequence
Database.
B. Keil, Cooperation between Databases and Scientific
Community.
Searching Databases:
W.R. Pearson, Rapid and Sensitive Sequence Comparison with FASTP
and FASTA.
R.F. Doolittle, Searching through Sequence Databases.
S. Henikoff, J.C. Wallace, and J.P. Brown, Finding Protein
Similarities with Nucleotide Sequence Databases.
C.B. Lawrence, Use of Homology Domains in Sequence Similarity
Detection.
M. Gribskov, R. L~aduthy, and D. Eisenberg, Profile Analysis.
Patterns in Nucleic Acid Sequences:
R. Staden, Finding Protein Coding Regions in Genomic
Sequences.
J.C.W. Shepherd, Ancient Patterns in Nucleic Acid Sequences.
R. Staden, Searching for Patterns in Protein and Nucleic Acid
Sequences.
G.D. Stormo, Consensus Patterns in DNA.
M.S. Waterman and R. Jones, Consensus Methods for DNA and Protein
Sequence Alignment.
J.-M. Claverie, I. Sauvaget, and L. Bougueleret, k-Tuple Frequency
Analysis: From Intron/Exon Discrimination to T-Cell Epitope
Mapping.
P. Senapathy, M.B. Shapiro, and N.L. Harris, Splice Junctions,
Branch Point Sites, and Exons: Sequence Statistics, Identification,
and Applications to Genome Project.
Predicting RNA Secondary Structures:
J.A. Jaeger, D.H. Turner, and M. Zuker, Predicting Optimal and
Suboptimal Secondary Structure for RNA.
H.M. Martinez, Detecting Pseudoknots and Other Local Base-Pairing
Structures in RNA Sequences.
D. Gautheret, F. Major, and R. Cedergren, Computer Modeling and
Display of RNA Secondary and Tertiary Structures.
Aligning Protein and Nucleic Acid Sequences:
D.G. George, W.C. Barker, and L.T. Hunt, Mutation Data Matrix and
Its Uses.
P. Argos and M. Vingron, Sensitivity Comparison of Protein Amino
Acid Sequences.
M. Murata, Three-Way Needleman-Wunsch Algorithm.
D.-F. Feng and R.F. Doolittle, Progressive Alignment and
Phylogenetic Tree Construction of Protein Sequences.
S. Karlin, B.E. Blaisdell, and V. Brendel, Identification of
Significant Sequence Patterns in Proteins.
G.J. Barton, Protein Multiple Sequence Alignment and Flexible
Pattern Matching.
D. Sankoff, R. Cedergren, and Y. Abel, Genomic Divergence through
Gene Rearrangement.
D.J. Bacon and W.F. Anderson, Multiple Sequence Comparison.
M. Vihinen, Simultaneous Comparison of Several Sequences.
W.R. Taylor, Hierarchical Method to Align Large Numbers of
Biological Sequences.
J.F. Collins and A.F.W. Coulson, Significance of Protein Sequence
Similarities.
G.M. Landau, U. Vishkin, and R. Nussinov, Fast Alignment of DNA and
Protein Sequences.
Estimating Sequence Divergence:
M. Eigen and R. Winkler-Oswatitsch, Statistical Geometry on
Sequence Space.
T. Gojobori, E.N. Moriyama, and M. Kimura, Statistical Methods for
Estimating Sequence Divergence.
H. Kishino and M. Hasegawa, Converting Distance to Time:
Application to Human Evolution.
C. Saccone, C. Lanave, G. Pesole, and G. Preparata, Influence of
Base Composition on Quantitative Estimates of Gene Evolution.
N. Saitou, Maximum Likelihood Methods.
Phylogenetic Trees:
J. Czelusniak, M. Goodman, N.D. Moncrief, and S.M. Kehoe, Maximum
Parsimony Approach to Construction of Evolutionary Trees from
Aligned Homologous Sequences.
P.L. Williams and W.M. Fitch, Phylogeny Determination Using
Dynamically Weighted Parsimony Method.
J. Hein, Unified Approach to Alignment and Phylogenies.
W.-H. Li and M. Gouy, Statistical Tests of Molecular
Phylogenies.
R.F. Doolittle and D.-F. Feng, Nearest Neighbor Procedure for
Relating Progressively Aligned Amino Acid Sequences.
M.S. Johnson, A. ~ajSali, and T.L. Blundell, Phylogenetic
Relationships from Three-Dimensional Protein Structures.
Each chapter includes references.
Author Index.
Subject Index.
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