Instant Notes in Bioinformatics

Overview of Bioinformatics
The scope of bioinformatics. Bioinformatics and the Internet
Useful bioinformatics sites on the WWW
Data Acquisition
Sequencing DNA, RNA and proteins
Determination of protein structure
Gene and protein expression data
Protein interaction data
Databases - Contents Structure and Annotation
File formats
Annotated sequence databases
Genome and organism-specific databases. Miscellaneous databases
Retrieval of Biological Data
Data retrieval with Entrez and DBGET/LinkDB
Data retrieval with SRS (sequence retrieval sequence)
Searching Sequence Databases by Sequence Similarity Criteria
Sequence similarity searches
Amino acid substitution matrices
Database searches: FASTA and BLAST
Sequence filters
Iterative database searches and PSI-BLAST
Multiple Sequence Alignment: Gene and Protein Families
Multiple sequence alignment and family relationships
Protein families and pattern databases
Protein domain families
Phylogenetics
Phylogenetics, cladistics and ontology
Building phylogenetic trees
Evolution of macromolecular sequences
Sequence Annotation
Principles of genome annotation
Annotation tools and resources
Structural Bioinformatics
Conceptual models of protein structure
The relationship of protein three-dimensional structure to protein function
The evolution of protein structure and function
Obtaining, viewing and analyzing structural data
Structural alignment
Classification of proteins of known three-dimensional structure: CATH and SCOP
Introduction to protein structure prediction
Structure prediction by comparative modeling
Secondary structure prediction
Advanced protein structure prediction and prediction strategies
Microarray Data Analysis
Microarray data: analysis method
Microarray data: tools and resources
Sequence sampling and SAGE
Proteomic Data Analysis
Analyzing data from 2-DE gels
Analyzing protein mass spectrometry data
Higher-Order Systems
Modeling and reconstructing molecular pathways
Protein interaction informatics
Higher-order models
Cheminformatics in Biology
Conventions for representing molecules
Cheminformatics resources
Bioinformatics in the Pharmaceutical Industry
Bioinformatics and drug discovery
Pharmainformatics resources
Basic Principles of Computing in Bioinformatics
Running computer software
Computer operating systems
Software downloading and installation
Database management
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