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Main.BIOL368 History
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December 04, 2008, at 03:15 PM
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# [[http://zucker.limbio-paris13.org/COURS/M1S1-SMBH/Cours2baba.html | Pairwise alignment applet]] November 17, 2008, at 06:33 PM
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# [[ http://bioinformatics.org/ctls/download/biol368/3.computational.thinking.zip| Computational thinking and computing in biology]]
November 11, 2008, at 01:43 PM
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# [[Microarray technology]]; [[http://www.bioinformatics.org/ctls/download/cases/yates.miRNA.zip|Case study on differential gene expression]]
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# [[ http://bioinformatics.org/ctls/download/biol368/ch18.functional.genomics.ppt| Microarray technology]]; [[http://www.bioinformatics.org/ctls/download/cases/yates.miRNA.zip|Case study on differential gene expression]]
November 11, 2008, at 01:34 PM
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# [[Microarray technology]] # [[http://www.bioinformatics.org/ctls/download/cases/yates.miRNA.zip|Case study on differential gene expression]]
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# [[Microarray technology]]; [[http://www.bioinformatics.org/ctls/download/cases/yates.miRNA.zip|Case study on differential gene expression]]
November 11, 2008, at 01:34 PM
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# [[Microarray technology]] # [[http://www.bioinformatics.org/ctls/download/cases/yates.miRNA.zip|Case study on differential gene expression]]
November 09, 2008, at 01:09 PM
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!! Course Materials (Slides based on materials from [[ http://www.bio.tamu.edu/FACMENU/FACULTY/XiongJ.htm |Jin Xiong]]) to:
!! Course Materials (Some slides are based on materials from [[ http://www.bio.tamu.edu/FACMENU/FACULTY/XiongJ.htm |Jin Xiong]]) November 09, 2008, at 01:06 PM
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# [[http://bioinformatics.org/ctls/download/biol368/1.R.intro.zip| Introduction to R]];
[[http://bioinformatics.org/ctls/download/biol368/2.R.programming.zip| Basic programming in R]]
to:
# [[http://bioinformatics.org/ctls/download/biol368/1.R.intro.zip| Introduction to R]], [[http://bioinformatics.org/ctls/download/biol368/2.R.programming.zip| Basic programming in R]]
November 09, 2008, at 01:05 PM
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# [[http://bioinformatics.org/ctls/download/biol368/1.R.intro.zip| Introduction to R]]
to:
# [[http://bioinformatics.org/ctls/download/biol368/1.R.intro.zip| Introduction to R]];
[[http://bioinformatics.org/ctls/download/biol368/2.R.programming.zip| Basic programming in R]]
November 05, 2008, at 10:01 PM
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# [[http://bioinformatics.org/ctls/download/biol368/1.R.intro.zip| Introduction to R]]
October 29, 2008, at 09:41 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch10.11.ppt | 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; [[http://bioinformatics.org/ctls/download/biol368/lab7.zip | Lab 7]]
# [[ http://bioinformatics.org/ctls/download/biol368/lab8.zip | Lab 8]]
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch10.11.ppt | 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; [[http://bioinformatics.org/ctls/download/biol368/lab7.zip | Lab 7]] [[ http://bioinformatics.org/ctls/download/biol368/lab8.zip | Lab 8]]
October 29, 2008, at 09:41 PM
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# [[ http://bioinformatics.org/ctls/download/biol368/lab8.zip | Lab 8]]
October 29, 2008, at 09:40 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch10.11.ppt | 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; [[http://bioinformatics.org/ctls/download/biol368/lab7.zip | Lab 7]] [[http://bioinformatics.org/ctls/download/biol368/hw6.doc | hw6]] ;
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch10.11.ppt | 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; [[http://bioinformatics.org/ctls/download/biol368/lab7.zip | Lab 7]]
October 29, 2008, at 09:39 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch10.11.ppt | 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; [[http://bioinformatics.org/ctls/download/biol368/lab7.zip | Lab 7]]
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch10.11.ppt | 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; [[http://bioinformatics.org/ctls/download/biol368/lab7.zip | Lab 7]] [[http://bioinformatics.org/ctls/download/biol368/hw6.doc | hw6]] ;
October 29, 2008, at 09:38 PM
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[[http://bioinformatics.org/ctls/download/biol368/hw6.doc | hw6]] ;
October 21, 2008, at 02:57 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch14.2nd.struc.prediction.ppt | Protein secondary structure prediction]], [[http://bioinformatics.org/ctls/download/biol368/ch15.protein.tertiary.struct.prediction.ppt | Protein tertiary structure prediction]] Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading; sliding window;
# [[http://bioinformatics.org/ctls/download/biol368/ch10.11.ppt | 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;
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch14.2nd.struc.prediction.ppt | Protein secondary structure prediction]], [[http://bioinformatics.org/ctls/download/biol368/ch15.protein.tertiary.struct.prediction.ppt | Protein tertiary structure prediction]] Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading; sliding window; [[http://bioinformatics.org/ctls/download/biol368/lab6.zip | Lab 6]]
# [[http://bioinformatics.org/ctls/download/biol368/ch10.11.ppt | 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; [[http://bioinformatics.org/ctls/download/biol368/lab7.zip | Lab 7]]
October 21, 2008, at 02:51 PM
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[[http://bioinformatics.org/ctls/download/biol368/hw5.doc | hw5]] ;
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[[http://bioinformatics.org/ctls/download/biol368/hw5.newick.doc | hw5]] ;
October 21, 2008, at 02:51 PM
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[[http://bioinformatics.org/ctls/download/biol368/hw5.doc | hw5]] ;
October 20, 2008, at 12:13 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch10.11.ppt | 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;
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch10.11.ppt | 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;
October 20, 2008, at 12:12 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch10.ppt | 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;
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch10.11.ppt | 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;
October 19, 2008, at 02:15 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch10.ppt | Basic Phylogeny]] Key topics: Trees; Newick format; Graph and Topology; Rooted and unrooted trees; Distancs;
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch10.ppt | 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;
October 19, 2008, at 01:33 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch14.2nd.struc.prediction.ppt | Protein secondary structure prediction]], [[http://bioinformatics.org/ctls/download/biol368/ch15.protein.tertiary.struct.prediction.ppt | Protein tertiary structure prediction]] Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading; moving window;
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch14.2nd.struc.prediction.ppt | Protein secondary structure prediction]], [[http://bioinformatics.org/ctls/download/biol368/ch15.protein.tertiary.struct.prediction.ppt | Protein tertiary structure prediction]] Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading; sliding window;
# [[http://bioinformatics.org/ctls/download/biol368/ch10.ppt | Basic Phylogeny]] Key topics: Trees; Newick format; Graph and Topology; Rooted and unrooted trees; Distancs;
October 08, 2008, at 04:59 PM
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October 08, 2008, at 04:57 PM
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October 07, 2008, at 05:12 PM
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* [[http://bioinformatics.org/ctls/download/biol368/hw1.database.doc | hw1]]
* [[http://bioinformatics.org/ctls/download/biol368/hw2.doc | hw2]]
* [[http://bioinformatics.org/ctls/download/biol368/hw3.doc | hw3]]
* [[http://bioinformatics.org/ctls/download/biol368/hw4.doc | hw4]]
to:
[[http://bioinformatics.org/ctls/download/biol368/hw1.database.doc | hw1]] ;
[[http://bioinformatics.org/ctls/download/biol368/hw2.doc | hw2]] ;
[[http://bioinformatics.org/ctls/download/biol368/hw3.doc | hw3]] ;
[[http://bioinformatics.org/ctls/download/biol368/hw4.doc | hw4]] ;
October 07, 2008, at 05:11 PM
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* [[http://bioinformatics.org/ctls/download/biol368/hw4.doc | hw4]]
October 07, 2008, at 10:59 AM
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# [[http://bioinformatics.org/ctls/download/biol368/ch14.2nd.struc.prediction.ppt | Protein secondary structure prediction]], [[http://bioinformatics.org/ctls/download/biol368/ch15.protein.tertiary.struct.prediction.ppt | Protein tertiary structure prediction]] Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading;
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch14.2nd.struc.prediction.ppt | Protein secondary structure prediction]], [[http://bioinformatics.org/ctls/download/biol368/ch15.protein.tertiary.struct.prediction.ppt | Protein tertiary structure prediction]] Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading; moving window;
October 06, 2008, at 08:18 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch14.2nd.struc.prediction.ppt | Protein secondary structure prediction]], [[http://bioinformatics.org/ctls/download/biol368/ch15.protein.tertiary.struc.prediction.ppt | Protein tertiary structure prediction]] Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading;
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch14.2nd.struc.prediction.ppt | Protein secondary structure prediction]], [[http://bioinformatics.org/ctls/download/biol368/ch15.protein.tertiary.struct.prediction.ppt | Protein tertiary structure prediction]] Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading;
October 06, 2008, at 08:16 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch13.ppt | Protein secondary structure prediction]], [[http://bioinformatics.org/ctls/download/biol368/ch14.ppt | Protein tertiary structure prediction]] Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading;
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch14.2nd.struc.prediction.ppt | Protein secondary structure prediction]], [[http://bioinformatics.org/ctls/download/biol368/ch15.protein.tertiary.struc.prediction.ppt | Protein tertiary structure prediction]] Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading;
October 06, 2008, at 07:55 PM
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# [[http://weblogo.berkeley.edu/ | WebLogo ]]
# [[http://spdbv.vital-it.ch/| SWISS PDB Viewer ]] Deleted lines 45-46:
# [[http://weblogo.berkeley.edu/ | WebLogo ]]
# [[http://spdbv.vital-it.ch/| SWISS PDB Viewer ]] October 06, 2008, at 07:36 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch13.ppt | Protein secondary structure prediction]],
[[http://bioinformatics.org/ctls/download/biol368/ch14.ppt | Protein tertiary structure prediction]] Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading;
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch13.ppt | Protein secondary structure prediction]], [[http://bioinformatics.org/ctls/download/biol368/ch14.ppt | Protein tertiary structure prediction]] Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading;
October 06, 2008, at 07:35 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch12.protein.structure.ppt | Protein structure basics]], [[http://bioinformatics.org/ctls/download/biol368/ch13.prot.struc.visualization.comparison.ppt | Visualization, Comparison]],[[http://bioinformatics.org/ctls/download/biol368/lab5.zip | Lab 5]]
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch12.protein.structure.ppt | Protein structure basics]], [[http://bioinformatics.org/ctls/download/biol368/ch13.prot.struc.visualization.comparison.ppt | Visualization, Comparison]],[[http://bioinformatics.org/ctls/download/biol368/lab5.zip | Lab 5]] Key topics: chirality, alpha helix, beta strand
# [[http://bioinformatics.org/ctls/download/biol368/ch13.ppt | Protein secondary structure prediction]],
[[http://bioinformatics.org/ctls/download/biol368/ch14.ppt | Protein tertiary structure prediction]] Key topics: Chou-Fasman method; false positive and false negative; homology modeling; threading;
---- October 01, 2008, at 10:39 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch12.protein.structure.ppt | Protein structure basics]], [[http://bioinformatics.org/ctls/download/biol368/ch13.prot.struc.visualization.comparison.ppt | Visulization, Comparison]],[[http://bioinformatics.org/ctls/download/biol368/lab5.zip | Lab 5]]
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch12.protein.structure.ppt | Protein structure basics]], [[http://bioinformatics.org/ctls/download/biol368/ch13.prot.struc.visualization.comparison.ppt | Visualization, Comparison]],[[http://bioinformatics.org/ctls/download/biol368/lab5.zip | Lab 5]]
October 01, 2008, at 10:38 PM
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# [[http://spdbv.vital-it.ch/| SWISS PDB Viewer ]] October 01, 2008, at 10:33 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch12.protein.structure.ppt | Protein structure basics]] [[http://bioinformatics.org/ctls/download/biol368/ch13.prot.struc.visualization.comparison.ppt | Visulization, Comparison]][[http://bioinformatics.org/ctls/download/biol368/lab5.zip | Lab 5]]
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch12.protein.structure.ppt | Protein structure basics]], [[http://bioinformatics.org/ctls/download/biol368/ch13.prot.struc.visualization.comparison.ppt | Visulization, Comparison]],[[http://bioinformatics.org/ctls/download/biol368/lab5.zip | Lab 5]]
October 01, 2008, at 10:33 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch12.protein.structure.ppt | Protein structure basics]] [[http://bioinformatics.org/ctls/download/biol368/ch13.prot.struc.visualization.comparison.ppt | Visulization, Comparison]]
[[http://bioinformatics.org/ctls/download/biol368/lab5.zip | Lab 5]]
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# [[http://bioinformatics.org/ctls/download/biol368/ch12.protein.structure.ppt | Protein structure basics]] [[http://bioinformatics.org/ctls/download/biol368/ch13.prot.struc.visualization.comparison.ppt | Visulization, Comparison]][[http://bioinformatics.org/ctls/download/biol368/lab5.zip | Lab 5]]
October 01, 2008, at 09:37 PM
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[[http://bioinformatics.org/ctls/download/biol368/lab5.zip | Lab 5]]
October 01, 2008, at 09:22 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch12.protein.structure.ppt | Protein structure basicus]] [[http://bioinformatics.org/ctls/download/biol368/ch13.prot.struc.visualization.and.comparison.ppt | Visuliation, Comparison]]
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch12.protein.structure.ppt | Protein structure basics]] [[http://bioinformatics.org/ctls/download/biol368/ch13.prot.struc.visualization.comparison.ppt | Visulization, Comparison]]
October 01, 2008, at 09:20 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch12.ppt | Protein structure basicus]] [[http://bioinformatics.org/ctls/download/biol368/ch12.ppt | Visuliation, Comparison]]
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch12.protein.structure.ppt | Protein structure basicus]] [[http://bioinformatics.org/ctls/download/biol368/ch13.prot.struc.visualization.and.comparison.ppt | Visuliation, Comparison]]
October 01, 2008, at 09:07 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch12.ppt | Protein structure basicus]] [[http://bioinformatics.org/ctls/download/biol368/ch12.ppt | Visuliation, Comparison]]
September 29, 2008, at 08:33 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch7.motif.and.domain.ppt | Protein domain and motif]] Key topics: PSSM; sequence logo;
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch7.motif.and.domain.ppt | Protein domain and motif]] Key topics: regular expression; PSSM; sequence logo;
September 29, 2008, at 08:31 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch7.ppt | Protein domain and motif]] Key topics: PSSM; sequence logo;
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# [[http://bioinformatics.org/ctls/download/biol368/ch7.motif.and.domain.ppt | Protein domain and motif]] Key topics: PSSM; sequence logo;
September 29, 2008, at 08:29 PM
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# [[http://weblogo.berkeley.edu/ | WebLogo ]] September 25, 2008, at 04:52 PM
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# [[http://www-ab.informatik.uni-tuebingen.de/software/dendroscope/welcome.html | Dendroscope ]] to:
# [[http://www-ab.informatik.uni-tuebingen.de/software/dendroscope/welcome.html | Dendroscope for tree presentation ]] September 25, 2008, at 04:51 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch7.ppt | Protein domain and motif]] Key topics: PSSM; sequence logo;
September 25, 2008, at 01:02 PM
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# [[http://www.phylogeny.fr/ | Online Phylogeny Construction ]]
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# [[http://www.phylogeny.fr/ | Online Phylogeny Construction, Marseille, France ]]
September 25, 2008, at 01:01 PM
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* [[http://www.ncbi.nlm.nih.gov/ | NCBI ]]
* [[http://blast.ncbi.nlm.nih.gov/Blast.cgi | NCBI BLAST ]]
* [[http://www.ebi.ac.uk/Tools/emboss/align/index.html | EBI Pairwise seq alignment ]]
* [[http://www.itu.dk/people/sestoft/bsa/graphalign.html | Graphic pairwise seq alignment by dynamic programming]]
* [[ http://www.ebi.ac.uk/Tools/clustalw/ | EBI ClustalW]]
* [[ http://www.megasoftware.net/ | MEGA4 ]]
* [[ http://www.geospiza.com/education/materials.html#data | Geospiza data ]]
* [[http://www.cs.umb.edu/~srevilak/viterbi/ | Viterbi Applet, UMB]]
* [[http://www-ab.informatik.uni-tuebingen.de/software/dendroscope/welcome.html | Dendroscope ]] to:
# [[http://www.ncbi.nlm.nih.gov/ | NCBI ]]
# [[http://blast.ncbi.nlm.nih.gov/Blast.cgi | NCBI BLAST ]]
# [[http://www.ebi.ac.uk/Tools/emboss/align/index.html | EBI Pairwise seq alignment ]]
# [[http://www.itu.dk/people/sestoft/bsa/graphalign.html | Graphic pairwise seq alignment by dynamic programming]]
# [[ http://www.ebi.ac.uk/Tools/clustalw/ | EBI ClustalW]]
# [[ http://www.megasoftware.net/ | MEGA4 ]]
# [[ http://www.geospiza.com/education/materials.html#data | Geospiza data ]]
# [[http://www.cs.umb.edu/~srevilak/viterbi/ | Viterbi Applet, UMB]]
# [[http://www-ab.informatik.uni-tuebingen.de/software/dendroscope/welcome.html | Dendroscope ]]
# [[http://www.phylogeny.fr/ | Online Phylogeny Construction ]]
September 23, 2008, at 11:23 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch6.Profiles.HMM.ppt | Profiles and HMM]] [[http://bioinformatics.org/ctls/download/biol368/lab4.psiblast.doc | Lab 4]] [[http://bioinformatics.org/ctls/download/biol368/hw3.doc | hw3]]
Key topics: PSSM; normalization; stochastic models; Markov chain; HMM; decoding;
to:
# [[http://bioinformatics.org/ctls/download/biol368/ch6.Profiles.HMM.ppt | Profiles and HMM]] [[http://bioinformatics.org/ctls/download/biol368/lab4.psiblast.doc | Lab 4]] [[http://bioinformatics.org/ctls/download/biol368/hw3.doc | hw3]] Key topics: PSSM; normalization; stochastic models; Markov chain; HMM; decoding;
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# [[http://bioinformatics.org/ctls/download/biol368/ch6.Profiles.HMM.ppt | Profiles and HMM]] [[http://bioinformatics.org/ctls/download/biol368/lab4.psiblast.doc | Lab 4]] to:
# [[http://bioinformatics.org/ctls/download/biol368/ch6.Profiles.HMM.ppt | Profiles and HMM]] [[http://bioinformatics.org/ctls/download/biol368/lab4.psiblast.doc | Lab 4]] [[http://bioinformatics.org/ctls/download/biol368/hw3.doc | hw3]] September 23, 2008, at 11:22 PM
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# [[http://bioinformatics.org/ctls/download/biol368/ch6.Profiles.HMM.ppt | Profiles and HMM]] Key topics: PSSM; normalization; stochastic models; Markov chain; HMM; decoding;
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# [[http://bioinformatics.org/ctls/download/biol368/ch6.Profiles.HMM.ppt | Profiles and HMM]] [[http://bioinformatics.org/ctls/download/biol368/lab4.psiblast.doc | Lab 4]]
Key topics: PSSM; normalization; stochastic models; Markov chain; HMM; decoding;
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* [[http://bioinformatics.org/ctls/download/biol368/hw3.doc | hw3]]
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# [[http://bioinformatics.org/ctls/download/biol368/ch6.Profiles.HMM.ppt | Profiles and HMM]] Key topics: PSSM; stochastic models; Markov chain; HMM; decoding;
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# [[http://bioinformatics.org/ctls/download/biol368/ch6.Profiles.HMM.ppt | Profiles and HMM]] Key topics: PSSM; normalization; stochastic models; Markov chain; HMM; decoding;
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# [[http://bioinformatics.org/ctls/download/biol368/chap6.Profiles.HMM.ppt | Profiles and HMM]] Key topics: PSSM; stochastic models; Markov chain; HMM; decoding;
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# [[http://bioinformatics.org/ctls/download/biol368/ch6.Profiles.HMM.ppt | Profiles and HMM]] Key topics: PSSM; stochastic models; Markov chain; HMM; decoding;
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# [[http://bioinformatics.org/ctls/download/biol368/chap6.Profiles.HMM.ppt | Multiple Alignment]] [[http://bioinformatics.org/ctls/download/biol368/lab3.blast.clustal.zip | Lab 3]]; Key topics: guide tree;
to:
# [[http://bioinformatics.org/ctls/download/biol368/chap6.Profiles.HMM.ppt | Profiles and HMM]] Key topics: PSSM; stochastic models; Markov chain; HMM; decoding;
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# [[http://bioinformatics.org/ctls/download/biol368/chap6.Profiles.HMM.ppt | Multiple Alignment]] [[http://bioinformatics.org/ctls/download/biol368/lab3.blast.clustal.zip | Lab 3]]; Key topics: guide tree;
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* [[http://www-ab.informatik.uni-tuebingen.de/software/dendroscope/welcome.html | Dendroscope ]] September 18, 2008, at 03:22 PM
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* [[http://www.cs.umb.edu/~srevilak/viterbi/ | Viterbi Applet, UMB]]
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# [[http://bioinformatics.org/ctls/download/biol368/chap5.multiple.alignment.ppt | Multiple Alignment]] [[http://bioinformatics.org/ctls/download/biol368/lab3.blast.clustal.zip | Lab 3 (BLAST and CLUSTAL)]]; Key topics: guide tree;
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# [[http://bioinformatics.org/ctls/download/biol368/chap5.multiple.alignment.ppt | Multiple Alignment]] [[http://bioinformatics.org/ctls/download/biol368/lab3.blast.clustal.zip | Lab 3]]; Key topics: guide tree;
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# [[http://bioinformatics.org/ctls/download/biol368/ch2.db.ppt | Database]] [[http://bioinformatics.org/ctls/download/biol368/hw1.database.doc | hw1 ]], [[http://bioinformatics.org/ctls/download/biol368/lab1.ncbi.doc | Lab 1 NCBI/Entrez]]
->Key topics: Relational database and tables, Abstraction
# [[http://bioinformatics.org/ctls/download/biol368/chap3.pairwise.seq.alignment.ppt | Pairwise alignment]], [[http://bioinformatics.org/ctls/download/biol368/hw2.doc | HW2]], [[http://bioinformatics.org/ctls/download/biol368/lab2.zip | Lab2]]
->Key topics: dot plot, dynamic programming, gap penalty, trace back, search space, BLOSUM
# [[http://bioinformatics.org/ctls/download/biol368/chap4.database.similarity.search.ppt | Database similarity search]]
->Key topics: Word; BLAST; E-value and database size; search space; filter of low-complexity region;
# [[http://bioinformatics.org/ctls/download/biol368/chap5.multiple.alignment.ppt | Multiple Alignment]] [[http://bioinformatics.org/ctls/download/biol368/lab3.blast.clustal.zip | Lab 3 (BLAST and CLUSTAL)]]
->Key topics: guide tree;
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# [[http://bioinformatics.org/ctls/download/biol368/ch2.db.ppt | Database]] [[http://bioinformatics.org/ctls/download/biol368/hw1.database.doc | hw1 ]], [[http://bioinformatics.org/ctls/download/biol368/lab1.ncbi.doc | Lab 1 NCBI/Entrez]]; Key topics: Relational database and tables, Abstraction
# [[http://bioinformatics.org/ctls/download/biol368/chap3.pairwise.seq.alignment.ppt | Pairwise alignment]], [[http://bioinformatics.org/ctls/download/biol368/hw2.doc | HW2]], [[http://bioinformatics.org/ctls/download/biol368/lab2.zip | Lab2]]; Key topics: dot plot, dynamic programming, gap penalty, trace back, search space, BLOSUM
# [[http://bioinformatics.org/ctls/download/biol368/chap4.database.similarity.search.ppt | Database similarity search]]; Key topics: Word; BLAST; E-value and database size; search space; filter of low-complexity region;
# [[http://bioinformatics.org/ctls/download/biol368/chap5.multiple.alignment.ppt | Multiple Alignment]] [[http://bioinformatics.org/ctls/download/biol368/lab3.blast.clustal.zip | Lab 3 (BLAST and CLUSTAL)]]; Key topics: guide tree;
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* [[http://bioinformatics.org/ctls/download/biol368/chap1.intro.ppt | Introduction]]
* [[http://bioinformatics.org/ctls/download/biol368/ch2.db.ppt | Database]] [[http://bioinformatics.org/ctls/download/biol368/hw1.database.doc | hw1 ]], [[http://bioinformatics.org/ctls/download/biol368/lab1.ncbi.doc | Lab 1 NCBI/Entrez]] to:
# [[http://bioinformatics.org/ctls/download/biol368/chap1.intro.ppt | Introduction]]
# [[http://bioinformatics.org/ctls/download/biol368/ch2.db.ppt | Database]] [[http://bioinformatics.org/ctls/download/biol368/hw1.database.doc | hw1 ]], [[http://bioinformatics.org/ctls/download/biol368/lab1.ncbi.doc | Lab 1 NCBI/Entrez]] Changed line 17 from:
* [[http://bioinformatics.org/ctls/download/biol368/chap3.pairwise.seq.alignment.ppt | Pairwise alignment]], [[http://bioinformatics.org/ctls/download/biol368/hw2.doc | HW2]], [[http://bioinformatics.org/ctls/download/biol368/lab2.zip | Lab2]] to:
# [[http://bioinformatics.org/ctls/download/biol368/chap3.pairwise.seq.alignment.ppt | Pairwise alignment]], [[http://bioinformatics.org/ctls/download/biol368/hw2.doc | HW2]], [[http://bioinformatics.org/ctls/download/biol368/lab2.zip | Lab2]] Changed line 20 from:
* [[http://bioinformatics.org/ctls/download/biol368/chap4.database.similarity.search.ppt | Database similarity search]] to:
# [[http://bioinformatics.org/ctls/download/biol368/chap4.database.similarity.search.ppt | Database similarity search]] Changed line 23 from:
* [[http://bioinformatics.org/ctls/download/biol368/chap5.multiple.alignment.ppt | Multiple Alignment]] [[http://bioinformatics.org/ctls/download/biol368/lab3.blast.clustal.zip | Lab 3 (BLAST and CLUSTAL)]] to:
# [[http://bioinformatics.org/ctls/download/biol368/chap5.multiple.alignment.ppt | Multiple Alignment]] [[http://bioinformatics.org/ctls/download/biol368/lab3.blast.clustal.zip | Lab 3 (BLAST and CLUSTAL)]] September 16, 2008, at 09:35 PM
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* [[http://bioinformatics.org/ctls/download/biol368/lab3.blast.clustal.zip | Lab 3, BLAST, CLUSTAL]]
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* [[http://bioinformatics.org/ctls/download/biol368/chap5.multiple.alignment.ppt | Multiple Alignment]] [[http://bioinformatics.org/ctls/download/biol368/lab3.blast.clustal.zip | Lab 3 (BLAST and CLUSTAL)]]
->Key topics: guide tree;
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* [[ http://www.geospiza.com/education/materials.html#data | Geospiza data ]]
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* [[ http://www.ebi.ac.uk/Tools/clustalw/ | MEGA4 ]] to:
* [[ http://www.ebi.ac.uk/Tools/clustalw/ | EBI ClustalW]] September 16, 2008, at 01:44 PM
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* [[ http://www.ebi.ac.uk/Tools/clustalw/ | MEGA4 ]] September 16, 2008, at 01:31 PM
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* [[ http://www.megasoftware.net/ | MEGA4 ]]
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* [[http://bioinformatics.org/ctls/download/biol368/lab3.blast.clustal.zip | Lab 3, BLAST, CLUSTAL]]
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* [[http://www.itu.dk/people/sestoft/bsa/graphalign.html | Graphic pairwise seq alignment]] to:
* [[http://www.itu.dk/people/sestoft/bsa/graphalign.html | Graphic pairwise seq alignment by dynamic programming]] September 15, 2008, at 10:58 PM
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* [[http://blast.ncbi.nlm.nih.gov/Blast.cgi | NCBI BLAST ]] September 11, 2008, at 11:30 AM
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* [[http://www.ebi.ac.uk/Tools/emboss/align/index.html | Pairwise seq alignment]] to:
* [[http://www.ebi.ac.uk/Tools/emboss/align/index.html | EBI Pairwise seq alignment ]] September 11, 2008, at 11:30 AM
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* [[http://genome.cs.mtu.edu/align/align.html | Pairwise seq alignment]] to:
* [[http://www.ebi.ac.uk/Tools/emboss/align/index.html | Pairwise seq alignment]] September 09, 2008, at 05:08 PM
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* [[http://bioinformatics.org/ctls/download/biol368/hw2.doc | hw2]]
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* [[http://bioinformatics.org/ctls/download/biol368/chap3.pairwise.seq.alignment.ppt | Pairwise alignment]], [[HW2]], [[http://bioinformatics.org/ctls/download/biol368/lab2.zip | Lab2]] to:
* [[http://bioinformatics.org/ctls/download/biol368/chap3.pairwise.seq.alignment.ppt | Pairwise alignment]], [[http://bioinformatics.org/ctls/download/biol368/hw2.doc | HW2]], [[http://bioinformatics.org/ctls/download/biol368/lab2.zip | Lab2]] September 09, 2008, at 05:07 PM
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* [[http://bioinformatics.org/ctls/download/biol368/chap3.pairwise.seq.alignment.ppt | Pairwise alignment]] to:
* [[http://bioinformatics.org/ctls/download/biol368/chap3.pairwise.seq.alignment.ppt | Pairwise alignment]], [[HW2]], [[http://bioinformatics.org/ctls/download/biol368/lab2.zip | Lab2]] September 09, 2008, at 02:47 PM
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!! Course Materials (Slides based on materials from Jin Xiong) to:
!! Course Materials (Slides based on materials from [[ http://www.bio.tamu.edu/FACMENU/FACULTY/XiongJ.htm |Jin Xiong]]) September 09, 2008, at 02:46 PM
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!! Course Materials (Slides based on materials from Jin Xiong) September 09, 2008, at 02:45 PM
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* [[http://bioinformatics.org/ctls/download/biol368/chap4.database.similarity.search.ppt | database similarity search]] to:
* [[http://bioinformatics.org/ctls/download/biol368/chap4.database.similarity.search.ppt | Database similarity search]] September 09, 2008, at 02:45 PM
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* [[database similarity search]] to:
* [[http://bioinformatics.org/ctls/download/biol368/chap4.database.similarity.search.ppt | database similarity search]] September 09, 2008, at 02:42 PM
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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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* [[database similarity search]]
->Key topics: WORD; BLAST
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!! Course Materials (based on slides from Jin Xiong) September 08, 2008, at 10:28 PM
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->Key topics: Relational database and tables, Abstraction Changed lines 15-16 from:
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->Key topics: dot plot, dynamic programming, gap penalty, trace back, search space, BLOSUM
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* [[http://bioinformatics.org/ctls/download/biol368/ch2.db.ppt | Database]],[[http://bioinformatics.org/ctls/download/biol368/hw1.database.doc | hw1 ]], [[http://bioinformatics.org/ctls/download/biol368/lab1.ncbi.doc | Lab 1 NCBI/Entrez]] to:
* [[http://bioinformatics.org/ctls/download/biol368/ch2.db.ppt | Database]] [[http://bioinformatics.org/ctls/download/biol368/hw1.database.doc | hw1 ]], [[http://bioinformatics.org/ctls/download/biol368/lab1.ncbi.doc | Lab 1 NCBI/Entrez]] September 08, 2008, at 10:04 PM
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* [[http://bioinformatics.org/ctls/download/biol368/ch2.db.ppt | Database]] to:
* [[http://bioinformatics.org/ctls/download/biol368/ch2.db.ppt | Database]],[[http://bioinformatics.org/ctls/download/biol368/hw1.database.doc | hw1 ]], [[http://bioinformatics.org/ctls/download/biol368/lab1.ncbi.doc | Lab 1 NCBI/Entrez]]
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* [[http://genome.cs.mtu.edu/align/align.html | Pairwise seq alignment]], [[http://bioinformatics.org/ctls/download/biol368/hw1.database.doc | hw1]], [[http://bioinformatics.org/ctls/download/biol368/lab1.ncbi.doc | Lab 1 NCBI/Entrez]] to:
* [[http://genome.cs.mtu.edu/align/align.html | Pairwise seq alignment]] September 08, 2008, at 10:02 PM
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* [[http://genome.cs.mtu.edu/align/align.html | Pairwise seq alignment]] to:
* [[http://genome.cs.mtu.edu/align/align.html | Pairwise seq alignment]], [[http://bioinformatics.org/ctls/download/biol368/hw1.database.doc | hw1]], [[http://bioinformatics.org/ctls/download/biol368/lab1.ncbi.doc | Lab 1 NCBI/Entrez]] September 08, 2008, at 05:31 PM
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* [[http://www.ncbi.nlm.nih.gov/ | NCBI ]] September 08, 2008, at 05:30 PM
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* [[http://www.itu.dk/people/sestoft/bsa/graphalign.html | Graphic seq alignment]] to:
* [[http://genome.cs.mtu.edu/align/align.html | Pairwise seq alignment]]
* [[http://www.itu.dk/people/sestoft/bsa/graphalign.html | Graphic pairwise seq alignment]] September 08, 2008, at 05:29 PM
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!! Useful sites
* [[http://www.itu.dk/people/sestoft/bsa/graphalign.html | Graphic seq alignment]]
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* [[http://bioinformatics.org/ctls/download/biol368/ch3.pairwise.seq.alignment.ppt | Pairwise alignment]] to:
* [[http://bioinformatics.org/ctls/download/biol368/chap3.pairwise.seq.alignment.ppt | Pairwise alignment]] September 03, 2008, at 09:25 PM
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* [[http://bioinformatics.org/ctls/download/biol368/ch3.pairwise.seq.alignment.ppt | Pairwise alignment]] September 03, 2008, at 12:39 PM
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!! Homeworks
* [[http://bioinformatics.org/ctls/download/biol368/hw1.database.doc | hw1]]
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!! %center%BIOL368 Introduction to Bionformatics
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!! %center%BIOL368 Introduction to Bioinformatics
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!! %center%BIOL368 Introduction to Biinformatics
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!! %center%BIOL368 Introduction to Bionformatics
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!! %center%BIOL368 Introduction to Bionformatics
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!! %center%BIOL368 Introduction to Biinformatics
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[[http://bioinformatics.org/ctls/download/0809.calendar.pdf | Academic Calendar]]
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* [[http://bioinformatics.org/ctls/download/biol368/ch2.db.ppt | Database]] August 27, 2008, at 12:15 PM
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!! %center%BIOL368 Introduction to Biinformatics
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!! %center%BIOL368 Introduction to Bionformatics
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!! %center%BIOL368 Introduction to Biinformatics
[[http://bioinformatics.org/ctls/download/biol368/368.syllabus.doc | BIOL368 syllabus ]]
[[http://bioinformatics.org/ctls/download/biol368/lab.policy.doc | Comp Lab Policy ]]
!! Course Materials
* [[http://bioinformatics.org/ctls/download/biol368/chap1.intro.ppt | Introduction]]
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