| week |
COURSE CONTENT |
REFERENCE MATERIALS |
|
1 |
Introduction What is Bioinformatics? Historical highlight Significance of Bioinformatics: Overview |
Xiong, J. (2006). Essential bioinformatics |
|
2 |
Data base and data bank search tools Overview of Biological databases Classification of data bases Sequence data bases DNA data base gen bank EMBL DDBJ Protein data base |
Attwood, T.K. (2004) Introduction to Bioinformatics |
|
3 |
Data search and mining tools |
Mani, k. and vijaraj N. (2003). Bioinformatics for beginners |
|
4 |
Nucleic acid sequence analysis Gene searching and sequence retrieval Sequence alignment BLAST ,MSA CLUSTALW X etc |
Rastogi et al., (2001). Bioinformatics: Methods and application |
|
5 |
Restriction analysis Primer designing |
Baxevanis, A.D. and Ouellette B. F. F. (2001). Bioinformatics a practical guide to the analysis of genes and proteins |
|
6 |
Protein sequence and structure analysis Protein sequence retrieval Protein sequence alignment |
Mani, k. and vijaraj N. (2003). Bioinformatics for beginners |
|
7 |
Protein structure prediction (primary secondary and tertiary) structure Protein structure visualization with RAMOL etc |
Baxevanis, A.D. and Ouellette B. F. F. (2001). Bioinformatics a practical guide to the analysis of genes and proteins |
|
8 |
Homology modeling |
Mani, k. and vijaraj N. (2003). Bioinformatics for beginners |
|
9 |
Application of bioinformatics Genome analysis Transcriptome analysis –micro array |
Baxevanis, A.D. and Ouellette B. F. F. (2001). Bioinformatics a practical guide to the analysis of genes and proteins |
|
10 |
Protein analysis |
Mani, k. and vijaraj N. (2003). Bioinformatics for beginners |
|
11 |
Metabolomics |
Baxevanis, A.D. and Ouellette B. F. F. (2001). Bioinformatics a practical guide to the analysis of genes and proteins |
|
12 |
Introduction to system biology |
Mani, k. and vijaraj N. (2003). Bioinformatics for beginners |
PRACTICAL CONTENTS
|
week |
CONTENT |
REFERENCE |
|
1 |
Web based exercise, Study of Public biological databases |
Data base |
|
2 |
Web base exercise, Primary sequences |
NCBI |
|
3 |
Web based exercise, Dot matrix plot |
NCBI and EBI |
|
4 |
Web based exercise Nucleotide translation |
NCBI |
|
5 |
Web based Searching for and identifying protein |
Web browsing |
|
6 |
Software exercise PSI-BLAST |
PSI-BLAST |
|
7 |
Alignment as a search tool |
NCBI &EBI |
|
8 |
Multiple sequence alignment |
All webs |
|
9 |
Gene finding |
Any web including ordinary web sites |
REQUIRED TEXT BOOKS AND MATERIALS
1. Xiong, J. (2006). Essential bioinformatics
2. Attwood, T.K. (2004) Introduction to Bioinformatics
3. Mani, k. and vijaraj N. (2003). Bioinformatics for beginners
4. Rastogi et al., (2001). Bioinformatics: Methods and application
5. Baxevanis, A.D. and Ouellette B. F. F. (2001). Bioinformatics a practical guide to the analysis of genes and proteins.
- Teacher: Alemayehu Letebo