Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences

This volume addresses a variety of areas in which computers are used to manage and manipulate nucleic acid and protein sequence data. The manipulations include searching, aligning, and determining the significance of similarities, as well as the construction of phylogenetic trees that show the evolutionary history of related sequences. Ready-to-use methods for the "at-the-bench" scientist are presented.

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.