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BIOL 368
BIOL368 Introduction to Bioinformatics
BIOL368 syllabus
Comp Lab Policy
Academic Calendar
Homeworks
hw1 ;
hw2 ;
hw3 ;
hw4 ;
hw5 ;
hw6 ;
Course Materials (Some slides are based on materials from Jin Xiong)
- Introduction
- Database hw1, Lab 1 NCBI/Entrez; Key topics: Relational database and tables, Abstraction
- Pairwise alignment, HW2, Lab2; Key topics: dot plot, dynamic programming, gap penalty, trace back, search space, BLOSUM
- Database similarity search; Key topics: Word; BLAST; E-value and database size; search space; filter of low-complexity region;
- Multiple Alignment Lab 3; Key topics: guide tree;
- Profiles and HMM Lab 4 hw3 Key topics: PSSM; normalization; stochastic models; Markov chain; HMM; decoding;
- Protein domain and motif Key topics: regular expression; PSSM; sequence logo;
- Protein structure basics, Visualization, Comparison,Lab 5 Key topics: chirality, alpha helix, beta strand
- Protein secondary structure prediction, Protein tertiary structure prediction Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading; sliding window; Lab 6
- Phylogeny Basics Key topics: Trees; Newick format; Graph and Topology; Rooted and unrooted trees; Ooutgroups; Synonymous and nonsynonymous substitution rates; Juke-Cantor distance; Kimura 2-parameter distance; UPGMA; Neighbour-joining; Maximum likelihood; Parsimony; Bootstrap; positive and negative selection; Lab 7 Lab 8
- Introduction to R, Basic programming in R
- Microarray technology; Case study on differential gene expression
- Computational thinking and computing in biology
Useful sites
- NCBI
- NCBI BLAST
- EBI Pairwise seq alignment
- Graphic pairwise seq alignment by dynamic programming
- Pairwise alignment applet
- EBI ClustalW
- MEGA4
- Geospiza data
- Viterbi Applet, UMB
- WebLogo
- SWISS PDB Viewer
- Dendroscope for tree presentation
- Online Phylogeny Construction, Marseille, France
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