Multiple alignments of Sequences and Structures using the T-Coffee framework

Weizmann Institute of Science, Rehovot, Israel, September 2008

Cedric Notredame

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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 ( 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.

Morning 1 (1h) LECTUREAn Introduction to Multiple Sequence AlignmentsL
Morning 1 (1h) PRACTICALBuilding Multiple Sequence Alignments on the webP
Morning 1 (1h) SEMINARAn Overview of T-CoffeeL
Morning 1 (1h) PRACTICALGuided Tour of the T-Coffee web serverP
Afternoon 1 (0.5h) PRACTICALInstalling T-Coffee LocallyP
Afternoon 1 (1h) PRACTICALAligning Sequences and Profiles with T-CoffeeP
Afternoon 1 (1h) SEMINARM-Coffee: Combining many methods into oneL
Afternoon 1 (1h) PRACTICALInstalling and Using M-CoffeeP
Morning 2 (1h) PRACTICALAdding a Novel Method to M-CoffeeP
Morning 2 (1h) SEMINARExpresso: Incorporating Structural Information in Multiple Sequence Alignments L
Morning 2 (1h) PRACTICALInstalling and Using Expresso P
Morning 2 (1h) SEMINARMultiple RNA Alignments with R-CoffeeL
Afternoon 2 (1h) PRACTICALInstalling and Using R-CoffeeP
Afternoon 2 (1h) SEMINARPost-Processing Multiple Sequence Alignments with T-Coffee
Afternoon 2 (2h) PRACTICALPractical Post Processing problems: Coloring, Extraction and RedundancyP