Bioinformatics 1, BIOL 4540/6540, Fall 2011

Syllabus
Here is the final checklist for Fall '11.
Study the homeworks and checklists for the final, which is comprehensive.
HW6 is posted.
Office hours W 10-12 or by appointment. Science Center room 3C07.
homework upload page

Lectures

√     What     When
√ Lecture 1    Thinking algorithmically.    PDF Aug 29, 2011
√ Lecture 2    Sequence databases. Sequencing. Dotplots. Motifs. Scoring.   PDF Sep 1, 2011 checklist
√ Lecture 3    Pairwise sequence alignment with gaps. Dynamic programming. PDF Sep 8, 2011
√ Lecture 4    Local versus global alignment. Multiple sequence alignment. PDF Sep 12, 2011 HW1 due
√ Lecture 5    Alignment scoring. Jukes-Cantor. BLOSUM, PAM.   PDF Sep 15, 2011 checklist
√ Lecture 6    Database searching. Indexing. FASTA and BLAST. PDF Sep 19, 2011 HW2 due
√ Lecture 7    Statistical Significance. E-values. PDF Sep 22, 2011
√ Lecture 8    Multiple sequence alignment. Clustal, Muscle. PDF Sep 26, 2011
√ Lecture 9    Editing multiple sequence alignments. bAliBase. PDF Sep 29, 2011
√ Lecture 10    Sequence weights, profiles and logos. PDF Oct 3, 2011 HW3 due
√ Lecture 11    review. PDF Oct 6, 2011 checklist
 
-------MIDTERM-------
 Oct 11, 2011
√ Lecture 13    watch a movie! DCC 330 Oct 13, 2011
√ Lecture 14    Phylogenetic analysis. Orthologs and paralogs. PDF Oct 17, 2011
√ Lecture 15    Parsimony. Maximum likelihood. Bootstrapping. PDF Oct 20, 2011
√ Lecture 16    The Tree of life. Monophyly and Paraphyly. PDF Oct 24, 2011
√ Lecture 17    Markov chains. Hidden Markov models. Profile HMMs. PDF Oct 27, 2011
√ Lecture 18    Footprints. Microrepeats, Transposons. Language models. PDF Oct 31, 2011 HW4 due
∅ Lecture 19    ...continued... Nov 3, 2011
∅ Lecture 20    ...continued... Nov 7, 2011
∅ Lecture 21    RNA secondary structure prediction. MFOLD. PDF1  PDF2 Nov 10, 2011 HW5 due
√ Lecture 22    Gene finding. Splicing. PDF Nov 14, 2011
∅ Lecture 23    PHYLIP workshop. PDF Nov 17, 2011 link
√ Lecture 24    Gene ontology. Sequence annotation.. PDF Nov 21, 2011
√ Lecture 25    Metagenomics. PDF Nov 28, 2011
√ Lecture 26    SNPs. Work on Projects PDF Dec 1, 2011
∅ Lecture 27    Work on Projects PDF Dec 5, 2011 HW6 due
 
----- Student presentations-----
 Dec 8, 2011
-------Final Exam-------
 Wed. Dec 14 3-6pm

Links etc

 Syllabus   Unix            
 Term Project 
K-means clustering Splicing 1 Splicing 2 ROC data
bad alignment GO SNPs    BLOSUM62 matrix
10000.dat Population talk
short DNA sequences LALIGN PRSS
Core course notes. Ethical stats problem mystery sequence Academic dishonesty
Evolution class, Dec 1. Lecture13_slide9 Course wiki page

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Last updated Thu Dec 1 13:35:30 EST 2011
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