Computer methods for macromolecular sequence analysis (1996)

Databases and Resources: B. Shomer, R.A.L. Harper, and G.N. Cameron, Information Services of European Bioinformatics Institute. O. White and A.R. Kerlavage, TDB: New Databases for Biological Discovery. D.G.George, L.T. Hunt, and W.C. Barker, PIR-International Protein Sequence Database. W.C. Barker, F. Pfeiffer, and D.G. George, Superfamily Classification in PIR-International Protein Sequence Database. C.H. Wu, Gene Classification ArtificialNeural System. J.G. Henikoff and S. Henikoff, Blocks Database and Its Applications. R. Staden, Indexing and Using Sequence Databases. T. Etzold, A. Ulyanov, and P. Argos, SRS: Information Retrieval System for Molecular Biology Data Banks. Searching through Databases: T.L. Madden, R.L. Tatusov, and J. Zhang, Applications of Network BLAST Server. G.D. Schuler, J.A. Epstein, H. Ohkawa, and J.A. Kans, Entrez: Molecular Biology Database and Retrieval System. P. Bork and T.J. Gibson, Applying Motif and Profile Searches. L. Patthy, Consensus Approaches in Detection of Distant Homologies. M. Gribskov and S. Veretnik, Identification of Sequence Patterns with Profile Analysis. J.-M. Claverie, Effective Large-Scale Sequence Similarity Searches. W.R. Pearson, Effective Protein Sequence Comparison. E.C. Uberbacher, Y. Xu, and R.J. Mural, Discovering and Understanding Genes in Human DNA Sequence Using GRAIL. G. Pesole, M. Attimonelli, and C. Saccone, Linguistic Analysis of Nucleotide Sequences: Algorithms for Pattern Recognition and Analysis of Codon Strategy. E.V. Koonin, R.L. Tatusov, and K.E. Rudd, Protein Sequence Comparison at Genome Scale. T.-M. Yi and E.S. Lander, IterativeTemplate Refinement: Protein-Fold Prediction Using Iterative Search and Hybrid Sequence/Structure Templates. Multiple Alignment and Phylogenetic Trees: W.R. Taylor, Multiple Protein Sequence Alignment: Algorithms and Gap Insertion. D.-F. Feng and R.F. Doolittle, Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them. D.G. Higgins, J.D. Thompson, and T.J. Gibson, Using CLUSTAL for Multiple Sequence Alignments. J. Hein and J. Stovlbuk, Combined DNA and Protein Alignment. J. Felsenstein, Inferring Phylogenies from Protein Sequences by Parsimony, Distance, and Likelihood Methods. N. Saitou, Reconstruction of Gene Trees from Sequence Data. W.-H. Li and X. Gu, Estimating Evolutionary Distances between DNA Sequences. S.F. Altschul and W. Gish, Local Alignment Statistics. D. Gusfield and P. Stelling, Parametric and Inverse-Parametric Sequence Alignment with XPARAL. Secondary Structure Considerations: C.D.Livingstone and G.J. Barton, Identification of Functional Residues and Secondary Structure from Protein Multiple Sequence Alignment. A. Lupas, Prediction and Analysis of Coiled-Coil Structures. B. Rost, PHD: Predicting One-Dimensional Protein Structure by Profile-Based Neural Networks. J. Garnier, J.-F. Gibrat, and B. Robson, GOR Method for Predicting Protein Secondary Structure from Amino Acid Sequence. J.C. Wootton and S. Federhen, Analysis of Compositionally Biased Regions in Sequence Databases. Three-Dimensional Considerations: M.S. Johnson, A.C.W. May, M.A. Rodionov, and J.P. Overington, Discrimination of Common Protein Folds: Application of Protein Structure to Sequence/Structure Comparisons. J.U. Bowie, K.Zhang, M. Wilmanns, and D. Eisenberg, Three-Dimensional Profiles for Measuring Compatability of Amino Acid Sequence with Three-Dimensional Structure. C.A. Orengo and W.R. Taylor, SSAP: Sequential Structure Alignment Program for Protein StructureComparison. S.E. Brenner, C. Chothia, T.J.P. Hubbard, and A.G. Murzin, Understanding Protein Structure: Using Scop for Fold Interpretation. M.B. Swindells, Detecting Structural Similarities: A User's Guide. L. Holm and C. Sander, Alignment of Three-Dimensional Protein Structures: Network Server for Database Searching. O. Poch and M. Delarue, Converting Sequence Block Alignments into Structural Insights. Author Index. Subject Index.