1. Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments
Olivier Poirot, Eamonn O'Toole and Cedric Notredame
Nucleic Acids Research, 31, (2003) July 22, 2003
Park, Ji-Yoon

2. Abstract
Web-based tool to the computation, the evaluation & combination of multiple alignment
The latest version of the T-Coffee package
Provided by Hewlet Packard & Centre National de la Recherche Scientifique
Can be used for align protein, RNA or DNA
100 sequences (2,000 residues long) process available

3. Related Publication
T-Coffee: A novel method for multiple sequence alignments. C.Notredame, D. Higgins, J. Heringa,Journal of Molecular Biology,Vol 302, pp ,2000 [pdf]
COFFEE: A New Objective Function For Multiple Sequence Alignmnent. C. Notredame, L. Holme and D.G. Higgins, Bioinformatics,Vol 14 (5) ,1998 [pdf]

5. Tcoffee

6. Methods
Multiple sequence alignment assembly - Given a set of pre-selected protein or DNA seq, computes a multiple seq alignment of the input sequences - By computing a collection of pair-wise alignment [ the best global alignment & 10 best local alignment ] - The highest level of consistency with alignment within the library
Computing a multiple alignment
- FASTA form sequence
Evaluating a multiple alignment
- evaluate pre-computed multiple sequence alignment
IV. Combine multiple alignments

7. Output of T-Coffee Computation

8. Colored Output of T-Coffee

9. Conclusion & Future Developments
A new multiple sequence alignment server
To produce high quality multiple sequence alignment
Further development
- Enhanced regarding the mixing of sequences & structure