Program for "Bioinformatics" spring 2008:

 

Module 1: "House-hold" Sequence Analysis Programs.

    Lecture: January 28 Introduction.
Features to expect from a general purpose sequence analysis program. In silico cloning with WinSeq.		 Material & Notes for
"Sequence Analysis Programs"
    Exercise: January 31

 

Module 2: Visit NIH/NCBI & Search in Databases. IB*)

    Lecture: February 4 ENTREZ: literature, sequences and much more. Database searches
Sequence formats, annotations
Pairwise alignment, BLAST 		Material & Notes for
"Database Searches"
    Exercise: February 7

 

Module 3: Phylogeny 1: Create a Phylogenetic Tree. IB*)

    Lecture: February 11 General principles; Distance methods.
Exercise: Create a phylogenetic tree with ClustalW and TreeDraw		 Material & Notes for
"Phylogeny 1"
    Exercise: February 18

There is no class on Feb. 14'th due to DIS Study Tours

 

Module 4: Phylogeny 2:

    Lecture: February 21 Parsimony analysis with Phylip and Maximum-likelihood analysis with Tree-Puzzle and Quality Assessment Material & Notes for
"Phylogeny 2"
    Exercise: February 25

 

Module 5: Gene-finding and Annotation. IB*)

    Lecture: February 28 Methods for prediction of genes in newly sequenced nucleotides.
GeneMark and other programs.		 Material & Notes for
"Gene Finding"
    Exercise: March 6

 

Midterm evaluation: "Phylogeny paper", deadline March 7.

 

Module 6: High Density Array Analysis 1

    Lecture: March 31 @ 9.15 Introduction to arrays: from colors to numbers.
 		 Material & Notes for
"Array 1"
    Exercise: March 31 @ 13.15

 

DIS Easter trips March 8'th through Marh 30'th; no class in this period.

 

Module 7: High Density Array Analysis 2

    Lecture: April 3 Introduction to arrays: from numbers to results.

 

 Material & Notes for
"Array 2"
    Exercise: April 7

 

Module 8: Predicting Protein Structure 1: Predicting Secondary Structures. IB*)

    Lecture: April 10 Secondary structures in Proteins
PredictProtein
Jpred2		 Material & Notes for
"Protein Structure 1"
    Exercise: April 14

 

Module 9: Predicting Protein Structure 2: Visualizing Tertiary Structure. IB*)

    Lecture: April 17 Visualization with the Swiss PDB viewer. Material & Notes for
"Protein Structure 2"
    Exercise: April 21

 

Module 10: Predicting Protein Structure 3: Modelling Tertiary Structure.

    Lecture: April 24 Threading with the Swiss PDB viewer. Material & Notes for
"Protein Structure 3"
    Exercise: April 28

 

Thursday May 1'st is a holiday in Denmark (Ascension Day); no class!

 

Module 11: Finding Motifs and Signals

    Lecture: May 5 Motif finding with various programs. Creation of Logo's. Material & notes for "Motif Finding"
    Exercise: May 8

 

IB*) These modules are also a part of the Introductory Bioinformatics course.

Array Analysis / Protein structure paper, Deadline May 16'th, 2008.

 

Information for the examination reports

Participants and Information on Student presentations; cake list 2008

Link to BSCW shared workspace (Requires password)

Course Announcement and Information

Participants in the spring 2007 course (should you wish to contact them)
Link to the 2007 course