An Introduction to Sequence Alignments |
This Entire Course Was Automatically Generated Using BED, the Bioinformatics Exercise Database. BED is a freeware available from cedric.notredame@europe.com |
This course is a primer on sequence alignments in the context of bioinformatics analysis. Students will learn about most of the basic techniques in bioinformatics, and how to use the web as a giant lab (the web-lab!) in which they can carry out biological experiments involving bioinformatics. Among other things they will learn how to run BLAST to find the sequences they need and how to use ClustalW or T-Coffee to make an analysis based on multiple sequence alignments. We will also describe in details dynamic programming, one of the most important algorithm in bioinformatic. All these tools will be presented in an evolutionnary context and several practical applications will be proposed. At the end of the course, students should know how to use the most basic sequence alignment methods while understanding their main limitations. |
| Date | Location | Session | Title | Links | |
| Tue. 29/05 | LECTURE | An Introduction to Pairwise Comparisons and Molecular Evolution | LL | ||
| Wed.30/05 | LECTURE | BLAST and its Many Flavors | L | ||
| Wed. 30/05 | PRACTICAL | Running BLAST | P | ||
| Thu. 31/05 | LECTURE | Advanced Modes of BLAST | L | ||
| Thu. 31/05 | PRACTICAL | Running PSI-BLAST | P | ||
| Fri. 1/06 | LECTURE | Pairwise Comparison Algorithms: SW and NW | L | ||
| Fri. 1/06 | PRACTICAL | Coding the Smith and Waterman Algorithm in Perl | P | ||
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| Mon. 04/06 | LECTURE | Multiple Sequence Alignments | L | ||
| Mon. 04/06 | PRACTICAL | Building and Using MSAs | P | ||
| Tue. 05/06 | LECTURE | Dressing up an Anonymous Sequence | L | ||
| Wed. 06/06 | PRACTICAL | Dressing up an Anonymous Sequence | P | ||
| Thu. 07/06 | SEMINAR | Recent Evolution of MSA algorithms | L | ||