Multiple alignments of Sequences and Structures using the T-Coffee framework |
This Entire Course Was Automatically Generated Using BED, the Bioinformatics Exercise Database. BED is a freeware available from Cedric Notredame |
This workshop is dedicated to the construction of multiple alignments with the T-Coffee package (www.tcoffee.org). T-Coffee is a versatile alignment tool that makes it possible to align sequences of DNA, structured ncRNAs or Protein, while combining sequence and structural information. One of the specificity of T-Coffee is its ability to combine several types of information such as primary structures, RNA secondary structures and protein tertiary structure. T-Coffee is also a versatile framework that makes it possible to seamlessly combine existing off-the-shelf method, thus providing all the necessary tools for building powerful and customized meta-methods such as M-Coffee. In the course of this workshop, we will see the algorithmic underlying principle of T-Coffee and its many extensions: 3D-Coffee, R-Coffee and M-Coffee. We will also cover the wide range of available multiple sequence alignment methods, highlighting the strengths and weaknesses of each of these. In the practical part, we will first introduce the default usage of T-Coffee, either via the web interface or using a command line local installation. We will then move toward more complex projects and show how novel methods can be introduced and combined within the T-Coffee framework. |
| Date | Location | Session | Title | Links | |
| Morning 1 (1h) | LECTURE | An Introduction to Multiple Sequence Alignments | L | ||
| Morning 1 (1h) | PRACTICAL | Building Multiple Sequence Alignments on the web | P | ||
| Morning 1 (1h) | SEMINAR | An Overview of T-Coffee | L | ||
| Morning 1 (1h) | PRACTICAL | Guided Tour of the T-Coffee web server | P | ||
| . | |||||
| Afternoon 1 (0.5h) | PRACTICAL | Installing T-Coffee Locally | P | ||
| Afternoon 1 (1h) | PRACTICAL | Aligning Sequences and Profiles with T-Coffee | P | ||
| Afternoon 1 (1h) | SEMINAR | M-Coffee: Combining many methods into one | L | ||
| Afternoon 1 (1h) | PRACTICAL | Installing and Using M-Coffee | P | ||
| . | |||||
| Morning 2 (1h) | PRACTICAL | Adding a Novel Method to M-Coffee | P | ||
| Morning 2 (1h) | SEMINAR | Expresso: Incorporating Structural Information in Multiple Sequence Alignments | L | ||
| Morning 2 (1h) | PRACTICAL | Installing and Using Expresso | P | ||
| Morning 2 (1h) | SEMINAR | Multiple RNA Alignments with R-Coffee | L | ||
| . | |||||
| Afternoon 2 (1h) | PRACTICAL | Installing and Using R-Coffee | P | ||
| Afternoon 2 (1h) | SEMINAR | Post-Processing Multiple Sequence Alignments with T-Coffee | |||
| Afternoon 2 (2h) | PRACTICAL | Practical Post Processing problems: Coloring, Extraction and Redundancy | P | ||