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Unit 1: Databases
- definition of bioinformatics
- structure/function of databases
- algorithms, scripting
- structure/function of the web
- hardware and software
- literature databases, search engines, Boolean logic
- DNA sequence databases, BLAST
- other database types (MMDB, GOLD, PDB, ecological)
- database structure, querying
- scripting
- internet as a research environment
- documentation requirements in bioinformatics
- NCBI, NBIF interfaces
- Perl tutorial
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Unit 2: Genomics
- retrieving and organizing data
- tools for genomic analysis
- problem-solving methods
- documenting observations
- genome structure/function
- DNA structure determination
- whole genome sequencing
- genome mapping & annotation
- comparative genomics
- analysis of raw sequencing data
- Sequencher
- gene finding software
- annotation software
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Unit 3: Molecular Genetics
- information flow in biosystems
- nucleic acid structure/function
- ethical issues in bioinformatics
- molecular medicine
- specialized software
- how disease genes are mapped
- linkage analysis
- polymorphism (SNP and RFLP)
- expression analysis by microarray
- plasmid mapping software
- primer design
- analysis of microarray with CrazyQuant, X-Cluster
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Unit 4: Phylogenetics
- molecular evolution
- statistical/probabilistic models
- generating hypotheses
- design of valid tests
- drawing valid conclusions
- methods of reconstructing evolutionary history
- tempo and mode in molecular evolution
- statistical/probabilistic models
- multiple sequence alignment
- analyzing drift vs selection
- tree building by parsimony and maximum likelihood
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Unit 5: Protein Structure Prediction
- protein structure/function
- physical/chemical properties
- motifs and profile methods
- structure databases
- 3D model building
- patterns in protein sequences
- structural correlates of motifs and profiles
- 3D protein structure determination
- model-building techniques
- SwissProt database, PDB
- motifs and profile analysis
- Modeller
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Unit 6: Metabolism & Networks
- integrative thinking
- software for large data sets
- data visualization
- commercial applications
- metabolic pathways, signaling
- metabolic pathway databases
- cell signaling network databases
- proteomic databases
- protein-protein interactions
- pharmaceutical data mining
- WIT metabolic database
- data-mining methods
- self-organizing maps
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