Introduction to Bioinformatics: A Theoretical and Practical Approach

SCG00039 SCG00040 Part I. Biochemistry, Cell, and Molecular Biology The Cell Nucleic Acids and Proteins: Modern Linguistics for the Genomics and Bioinformatics Era Structure and Function of Cell Organelles Cell Signaling B. Transcription and Translation DNA Replication, Repair, and Recombination Transcription, RNA Processing, and Translation Part II. Molecular Genetics Genomics Epigenetic Mechanisms Regulating Gene Expression Gene Families and Evolution Repetitive DNA: Detection, Annotation, and Analysis Molecular Genetics of Disease and the Human Genome Project Clinical Human Genetics The Clinical Genetics Databases Population Genetics Part III. The UNIX Operating System Basics and Installation Introduction to UNIX for Biologists Installation of the Sun Solaris™ Operating Environment Sun System Administration Managing Bioinformatics Tools Installing Bioinformatics Software in a Server-Based Computing Environment Management of a Server-Based Bioinformatics Resource C. Command Line Sequence Analysis GCG File Management GCG Sequence Analysis Part IV. Computer Applications A. Management and Analysis of DNA Sequencing Projects and Sequences Managing Sequencing Projects in the GAP4 Environment OLIGO Primer Analysis Software Statistical Modeling of DNA Sequences and Patterns Statistical Mining of the Matrix Attachment Regions in Genomic Sequences Analyzing Sequences Using the Staden Package and EMBOSS B. The Genome Database: Analysis and Similarity Searching Ensembl: An Open-Source Software Tool for Large-Scale Genome Analysis The PIR for Functional Genomics and Proteomics Sequence Similarity and Database Searching GCG Database Searching C. Identifying Functional and Structural Sequence Elements Pattern Discovery: Methods and Software The Role of Transcription Factor Binding Sites in Promoters and Their In Silico Detection An Introduction to Multiple Sequence Alignment and Analysis 3D Molecular Visualization with Protein Explorer Multiple Sequence Alignment and Analysis: The SeqLab Interface: A Practical Guide D. Analysis of Gene Expression: Microarrays and Other Tools Overview of the Tools for Microarray Analysis: Transcription Profiling, DNA Chips, and Differential Display Microarrays: Tools for Gene Expression Analysis Knowledge Discovery from the Human Transcriptome Part V. Appendices Appendix 1: CD Contents Appendix 2: A Collection of Useful Bioinformatic Tools and Molecular Tables Appendix 3: Simple UNIX Commands