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.
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 effective. We also conclude that for a web server with moderate usage (10K hits/month) the cloud provides a cost-effective alternative to in-house deployment.Availability: T-Coffee is a freeware open source package available from http://www.tcoffee.org/homepage.htmlContact: cedric.notredame@crg.es
Multiple sequence alignment (MSA) is one of the most useful tools in bioinformatics. MSA plays a key role in protein/RNA structure prediction, phylogenetic analysis or pattern identification among other important bioinformatic applications. However, the growth of sequencing data imposes further difficulties to aligning it with traditional tools. For large-scale alignments with thousands of sequences or even whole genomes, it will be necessary to use and take advantage of high performance computing (HPC). This paper, focused on a consistency-based MSA tool called T-Coffee, presents several innovative solutions; the Balanced Guide Tree, the Optimized Library Method and the Multiple Tree Alignment. The results obtained by the methods presented have demonstrated that it is possible to improve efficiency, scalability and accuracy.
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