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Software design
T-Coffee is an open source freeware. It can
generate multiple sequence alignment for a given a
set of sequences (Protein, RNA or DNA). The latest
version of T-Coffee is 5.65. It runs on UNIX or
Microsoft Windows/Cywin. Version 2.00 and
higher can combine sequences and structures. It
uses bioperl in the design. The interface is self
explanatory with no complicated terms and
expression. EXPRESSO aligns the structures using
SAP, a program from Taylor and Orengo, and it
aligns sequences and structures using FUGUE, a
threading package from Kenji Mizuguchi
(developed in Tom Blundell’s lab at Cambridge
University). CORE server on www.tcoffee.org can
evaluate the quality of any multiple sequence
alignments with any of the most common formats
(MSF, ALN, FASTA, and PIR).
Limitations in use
- The input for Tcoffee is limited to a maximum
number of sequences of 50 and the maximum
length of sequences of 2000.
- The data will remain available on the server for
only nine days. Then it will be deleted.
- It is very important to cite the Tcoffee authors
when using its resources. For instance, if you
use the local version of Tcoffee, cite the
following paper:-
Notredame, D. Higgins, J. Heringa . T-Coffee: A
novel method for multiple sequence alignments.
Journal of Molecular Biology, Vol 302, pp205-
217,2000.
Otherwise, cite the paper that corresponds to the
server you have been using (click on the "cite"
button associated with every server on
www.tcoffee.org).
New features, flavors and tools of Tcoffee
Alignment
TCOFFEE (Regular or advanced): Computes a
multiple sequence alignment and the associated
phylogenetic tree.
EXPRESSO (3DCoffee) (Regular or advanced):
This server computes structure based Multiple
Sequence Alignments.
MCOFFEE (Regular or advanced): Computes a
multiple sequence alignment and the associated
phylogenetic tree by combining the output of
several multiple sequence alignment packages
(PCMA, Poa, Mafft, Muscle, T-Coffee,
ClustalW, ProbCons, DialignT).
COMBINE (Regular or advanced): combines two
(or more) multiple sequence alignments into a
single one.
RCOFFEE (Regular or advanced): Multiple
Sequence Alignment of Non Coding RNA
Sequences using RNAplfold predicted
secondary structures.
Evaluation
CORE (Regular or advanced): evaluates your
Alignment and outputs a colored version where
bad portions are in blue and the good ones in
red. Your alignment must contain at least four
sequences
iRMSD-APDB (Regular or advanced): Evaluates
your Multiple Sequence Alignment using
APDB which estimates the proportion of
columns correctly aligned in a pairwise or a
multiple alignment of sequences with known
structures.
List of Tcoffee servers availability around
the world
- www.tcoffee.org
- http://tcoffee.vital-it.ch/cgibin/Tcoffee/tcoffee_cgi/index.cgi
- http://www.es.embnet.org/Services/MolBio/tcoffee/
- http://www.ebi.ac.uk/t-coffee/
Ahmed MANSOUR
Genetics Department,
Faculty of Agriculture,
Zagazig University, Egypt
(author for correspondence; amansour@zu.edu.eg)
Received: 27 March 2008; Accepted: 11 December 2009