Main.BIOL368 History

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December 04, 2008, at 03:15 PM by 192.203.127.3 -
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  1. Pairwise alignment applet
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November 17, 2008, at 06:33 PM by 192.203.127.3 -
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  1. Computational thinking and computing in biology
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November 11, 2008, at 01:43 PM by 192.203.127.3 -
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  1. Microarray technology?; Case study on differential gene expression
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  1. Microarray technology; Case study on differential gene expression
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November 11, 2008, at 01:34 PM by 192.203.127.3 -
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  1. Microarray technology? # Case study on differential gene expression
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  1. Microarray technology?; Case study on differential gene expression
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November 11, 2008, at 01:34 PM by 192.203.127.3 -
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  1. Microarray technology? # Case study on differential gene expression
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November 09, 2008, at 01:09 PM by 76.123.119.30 -
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Course Materials (Slides based on materials from Jin Xiong)

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Course Materials (Some slides are based on materials from Jin Xiong)

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November 09, 2008, at 01:06 PM by 76.123.119.30 -
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  1. Introduction to R; 
 Basic programming in R
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  1. Introduction to R, Basic programming in R
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November 09, 2008, at 01:05 PM by 76.123.119.30 -
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  1. Introduction to R

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  1. Introduction to R; 
 Basic programming in R
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November 05, 2008, at 10:01 PM by 75.143.68.139 -
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  1. Introduction to R

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October 29, 2008, at 09:41 PM by 75.143.68.139 -
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  1. 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
  2. Lab 8

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  1. 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

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October 29, 2008, at 09:41 PM by 75.143.68.139 -
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  1. Lab 8

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October 29, 2008, at 09:40 PM by 75.143.68.139 -
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  1. 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 hw6 ;

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  1. 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

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October 29, 2008, at 09:39 PM by 75.143.68.139 -
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  1. 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

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  1. 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 hw6 ;

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October 29, 2008, at 09:38 PM by 75.143.68.139 -
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hw6 ;

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October 21, 2008, at 02:57 PM by 192.203.127.3 -
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  1. Protein secondary structure prediction, Protein tertiary structure prediction Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading; sliding window;

  2. 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;

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  1. 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

  2. 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

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October 21, 2008, at 02:51 PM by 192.203.127.3 -
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hw5 ;

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hw5 ;

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October 21, 2008, at 02:51 PM by 192.203.127.3 -
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hw5 ;

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October 20, 2008, at 12:13 PM by 75.143.68.139 -
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  1. 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;

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  1. 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;

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October 20, 2008, at 12:12 PM by 75.143.68.139 -
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  1. 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;

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  1. 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;

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October 19, 2008, at 02:15 PM by 76.123.119.30 -
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  1. Basic Phylogeny Key topics: Trees; Newick format; Graph and Topology; Rooted and unrooted trees; Distancs;
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  1. 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;

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October 19, 2008, at 01:33 PM by 76.123.119.30 -
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  1. Protein secondary structure prediction, Protein tertiary structure prediction Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading; moving window;

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  1. Protein secondary structure prediction, Protein tertiary structure prediction Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading; sliding window;

  2. Basic Phylogeny Key topics: Trees; Newick format; Graph and Topology; Rooted and unrooted trees; Distancs;
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October 08, 2008, at 04:59 PM by 75.143.68.139 -
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Attache:hw4.doc

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October 08, 2008, at 04:57 PM by 75.143.68.139 -
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Attache:hw4.doc

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October 07, 2008, at 05:12 PM by 192.203.127.3 -
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hw1 ; hw2 ; hw3 ; hw4 ;

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October 07, 2008, at 05:11 PM by 192.203.127.3 -
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  • hw4
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October 07, 2008, at 10:59 AM by 192.203.127.3 -
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  1. Protein secondary structure prediction, Protein tertiary structure prediction Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading;

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  1. Protein secondary structure prediction, Protein tertiary structure prediction Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading; moving window;

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October 06, 2008, at 08:18 PM by 75.143.68.139 -
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  1. Protein secondary structure prediction, Protein tertiary structure prediction Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading;

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  1. Protein secondary structure prediction, Protein tertiary structure prediction Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading;

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October 06, 2008, at 08:16 PM by 75.143.68.139 -
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  1. Protein secondary structure prediction, Protein tertiary structure prediction Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading;

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  1. Protein secondary structure prediction, Protein tertiary structure prediction Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading;

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October 06, 2008, at 07:55 PM by 75.143.68.139 -
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  1. WebLogo
  2. SWISS PDB Viewer
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  1. WebLogo
  2. SWISS PDB Viewer
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October 06, 2008, at 07:36 PM by 75.143.68.139 -
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  1. Protein secondary structure prediction,

Protein tertiary structure prediction Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading;

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  1. Protein secondary structure prediction, Protein tertiary structure prediction Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading;

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October 06, 2008, at 07:35 PM by 75.143.68.139 -
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  1. Protein structure basics, Visualization, Comparison,Lab 5

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  1. Protein structure basics, Visualization, Comparison,Lab 5 Key topics: chirality, alpha helix, beta strand

  2. Protein secondary structure prediction,

Protein tertiary structure prediction Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading;

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October 01, 2008, at 10:39 PM by 75.143.68.139 -
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  1. Protein structure basics, Visulization, Comparison,Lab 5

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  1. Protein structure basics, Visualization, Comparison,Lab 5

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October 01, 2008, at 10:38 PM by 75.143.68.139 -
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  1. SWISS PDB Viewer
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October 01, 2008, at 10:33 PM by 75.143.68.139 -
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  1. Protein structure basics Visulization, ComparisonLab 5

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  1. Protein structure basics, Visulization, Comparison,Lab 5

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October 01, 2008, at 10:33 PM by 75.143.68.139 -
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  1. Protein structure basics Visulization, Comparison

Lab 5

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  1. Protein structure basics Visulization, ComparisonLab 5

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October 01, 2008, at 09:37 PM by 75.143.68.139 -
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Lab 5

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October 01, 2008, at 09:22 PM by 75.143.68.139 -
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  1. Protein structure basicus Visuliation, Comparison
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  1. Protein structure basics Visulization, Comparison
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October 01, 2008, at 09:20 PM by 75.143.68.139 -
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  1. Protein structure basicus Visuliation, Comparison

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  1. Protein structure basicus Visuliation, Comparison
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October 01, 2008, at 09:07 PM by 75.143.68.139 -
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  1. Protein structure basicus Visuliation, Comparison

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September 29, 2008, at 08:33 PM by 75.143.68.139 -
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  1. Protein domain and motif Key topics: PSSM; sequence logo;
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  1. Protein domain and motif Key topics: regular expression; PSSM; sequence logo;
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September 29, 2008, at 08:31 PM by 75.143.68.139 -
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  1. Protein domain and motif Key topics: PSSM; sequence logo;
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  1. Protein domain and motif Key topics: PSSM; sequence logo;
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September 29, 2008, at 08:29 PM by 75.143.68.139 -
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  1. WebLogo
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September 25, 2008, at 04:52 PM by 192.203.127.3 -
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  1. Dendroscope
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  1. Dendroscope for tree presentation
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September 25, 2008, at 04:51 PM by 192.203.127.3 -
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  1. Protein domain and motif Key topics: PSSM; sequence logo;
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September 25, 2008, at 01:02 PM by 192.203.127.3 -
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  1. Online Phylogeny Construction
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  1. Online Phylogeny Construction, Marseille, France
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September 25, 2008, at 01:01 PM by 192.203.127.3 -
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  • NCBI
  • NCBI BLAST
  • EBI Pairwise seq alignment
  • Graphic pairwise seq alignment by dynamic programming
  • EBI ClustalW
  • MEGA4
  • Geospiza data
  • Viterbi Applet, UMB
  • Dendroscope
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  1. NCBI
  2. NCBI BLAST
  3. EBI Pairwise seq alignment
  4. Graphic pairwise seq alignment by dynamic programming
  5. EBI ClustalW
  6. MEGA4
  7. Geospiza data
  8. Viterbi Applet, UMB
  9. Dendroscope
  10. Online Phylogeny Construction
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September 23, 2008, at 11:23 PM by 75.143.68.139 -
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  1. Profiles and HMM Lab 4 hw3

Key topics: PSSM; normalization; stochastic models; Markov chain; HMM; decoding;

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  1. Profiles and HMM Lab 4 hw3 Key topics: PSSM; normalization; stochastic models; Markov chain; HMM; decoding;

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September 23, 2008, at 11:23 PM by 75.143.68.139 -
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  1. Profiles and HMM Lab 4
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  1. Profiles and HMM Lab 4 hw3
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  1. Profiles and HMM Key topics: PSSM; normalization; stochastic models; Markov chain; HMM; decoding;

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  1. Profiles and HMM Lab 4

Key topics: PSSM; normalization; stochastic models; Markov chain; HMM; decoding;

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September 23, 2008, at 10:57 PM by 75.143.68.139 -
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  • hw3
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September 23, 2008, at 11:53 AM by 192.203.127.3 -
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  1. Profiles and HMM Key topics: PSSM; stochastic models; Markov chain; HMM; decoding;

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  1. Profiles and HMM Key topics: PSSM; normalization; stochastic models; Markov chain; HMM; decoding;

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September 23, 2008, at 10:04 AM by 192.203.127.3 -
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  1. Profiles and HMM Key topics: PSSM; stochastic models; Markov chain; HMM; decoding;

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  1. Profiles and HMM Key topics: PSSM; stochastic models; Markov chain; HMM; decoding;

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September 22, 2008, at 09:52 PM by 75.143.68.139 -
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  1. Multiple Alignment Lab 3; Key topics: guide tree;

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  1. Profiles and HMM Key topics: PSSM; stochastic models; Markov chain; HMM; decoding;

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  1. Multiple Alignment Lab 3; Key topics: guide tree;

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September 20, 2008, at 09:27 PM by 76.123.119.30 -
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  • Dendroscope
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September 18, 2008, at 03:22 PM by 192.203.127.3 -
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  • Viterbi Applet, UMB
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  1. Multiple Alignment Lab 3 (BLAST and CLUSTAL); Key topics: guide tree;

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  1. Multiple Alignment Lab 3; Key topics: guide tree;

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September 16, 2008, at 09:38 PM by 75.143.68.139 -
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  1. Database hw1, Lab 1 NCBI/Entrez
Key topics: Relational database and tables, Abstraction

  1. Pairwise alignment, HW2, Lab2
Key topics: dot plot, dynamic programming, gap penalty, trace back, search space, BLOSUM

  1. Database similarity search
Key topics: Word; BLAST; E-value and database size; search space; filter of low-complexity region;

  1. Multiple Alignment Lab 3 (BLAST and CLUSTAL)
Key topics: guide tree;

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  1. Database hw1, Lab 1 NCBI/Entrez; Key topics: Relational database and tables, Abstraction

  2. Pairwise alignment, HW2, Lab2; Key topics: dot plot, dynamic programming, gap penalty, trace back, search space, BLOSUM

  3. Database similarity search; Key topics: Word; BLAST; E-value and database size; search space; filter of low-complexity region;

  4. Multiple Alignment Lab 3 (BLAST and CLUSTAL); Key topics: guide tree;

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  • Introduction

  • Database hw1, Lab 1 NCBI/Entrez
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  1. Introduction

  2. Database hw1, Lab 1 NCBI/Entrez
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  • Pairwise alignment, HW2, Lab2
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  1. Pairwise alignment, HW2, Lab2
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  • Database similarity search
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  1. Database similarity search
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  • Multiple Alignment Lab 3 (BLAST and CLUSTAL)
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  1. Multiple Alignment Lab 3 (BLAST and CLUSTAL)
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  • Lab 3, BLAST, CLUSTAL

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  • Multiple Alignment Lab 3 (BLAST and CLUSTAL)

Key topics: guide tree;

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September 16, 2008, at 04:47 PM by 192.203.127.3 -
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  • Geospiza data

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  • MEGA4
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  • EBI ClustalW
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September 16, 2008, at 01:44 PM by 192.203.127.3 -
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  • MEGA4
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  • MEGA4
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  • Lab 3, BLAST, CLUSTAL

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  • Graphic pairwise seq alignment
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  • Graphic pairwise seq alignment by dynamic programming
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September 15, 2008, at 10:58 PM by 75.143.68.139 -
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  • NCBI BLAST
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  • Pairwise seq alignment
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  • EBI Pairwise seq alignment
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September 11, 2008, at 11:30 AM by 192.203.127.3 -
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  • Pairwise seq alignment
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  • Pairwise seq alignment
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September 09, 2008, at 05:08 PM by 192.203.127.3 -
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  • hw2
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  • Pairwise alignment, HW2?, Lab2
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  • Pairwise alignment, HW2, Lab2
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  • Pairwise alignment
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  • Pairwise alignment, HW2?, Lab2
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Course Materials (Slides based on materials from Jin Xiong)

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Course Materials (Slides based on materials from Jin Xiong)

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Course Materials (based on slides from Jin Xiong)

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Course Materials (Slides based on materials from Jin Xiong)

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  • database similarity search
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  • Database similarity search
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  • database similarity search
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Key topics: Word; BLAST

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Key topics: Word; BLAST; E-value and database size; search space; filter of low-complexity region;

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Key topics: WORD; BLAST

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Key topics: Word; BLAST

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Key topics: WORD; BLAST

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Course Materials

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Course Materials (based on slides from Jin Xiong)

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Key topics: Relational database and tables, Abstraction
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Key topics: dot plot, dynamic programming, gap penalty, trace back, search space, BLOSUM
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  • Database,hw1, Lab 1 NCBI/Entrez
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  • Database hw1, Lab 1 NCBI/Entrez
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  • Database
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  • Database,hw1, Lab 1 NCBI/Entrez
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  • Pairwise seq alignment, hw1, Lab 1 NCBI/Entrez
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  • Pairwise seq alignment
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  • Pairwise seq alignment
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  • Pairwise seq alignment, hw1, Lab 1 NCBI/Entrez
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  • NCBI
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  • Graphic seq alignment
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  • Pairwise seq alignment
  • Graphic pairwise seq alignment
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Useful sites

  • Graphic seq alignment
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  • Pairwise alignment
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  • Pairwise alignment
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  • Pairwise alignment
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Homeworks

  • hw1
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BIOL368 Introduction to Bionformatics

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BIOL368 Introduction to Bioinformatics

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BIOL368 Introduction to Biinformatics

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BIOL368 Introduction to Bionformatics

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BIOL368 Introduction to Bionformatics

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BIOL368 Introduction to Biinformatics

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 Academic Calendar
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  • Database
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BIOL368 Introduction to Biinformatics

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BIOL368 Introduction to Bionformatics

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BIOL368 Introduction to Biinformatics

 BIOL368 syllabus

 Comp Lab Policy

Course Materials

  • Introduction
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