T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension
Di Tommaso, Paolo
Montañola Lacort, Alberto
MetadataShow full item record
This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee
mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10 000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.
Is part ofNucleic Acids Research, 2011, vol. 39, supl. 2 (Web Server issue), W13-17
The following license files are associated with this item:
Except where otherwise noted, this item's license is described as cc-by-nc, (c) Di Tommaso et al., 2011
Showing items related by title, author, creator and subject.
High Performance computing improvements on bioinformatics consistency-based multiple sequence alignment tools Orobitg Cortada, Miquel; Guirado Fernández, Fernando; Cores Prado, Fernando; Lladós Segura, Jordi; Notredame, Cedric (Elsevier, 2014-10-08)Multiple Sequence Alignment (MSA) is essential for a wide range of applications in Bioinformatics. Traditionally, the alignment accuracy was the main metric used to evaluate the goodness of MSA tools. However, with the ...
Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud Di Tommaso, Paolo; Orobitg Cortada, Miquel; Guirado Fernández, Fernando; Cores Prado, Fernando; Espinosa, Toni; Notredame, Cedric (Oxford University Press, 2010)Summary: We present the first parallel implementation of the T-Coffee consistency-based multiple aligner. We benchmark it on the Amazon Elastic Cloud (EC2) and show that the parallelization procedure is reasonably ...
Orobitg Cortada, Miquel; Guirado Fernández, Fernando; Notredame, Cedric; Cores Prado, Fernando (Springer Verlag, 2011)Multiple Sequence Alignment (MSA) constitutes an extremely powerful tool for important biological applications such as phylogenetic analysis, identification of conserved motifs and domains and structure prediction. In ...