Journal of Cell and Molecular Biology 7(2) & 8(1): 71-72, 2010 Haliç University, Printed in Turkey. http://jcmb.halic.edu.tr
Software Review
Tcoffee ©: Multipurpose sequence alignments program Authors: C. NOTREDAME, L. HOLME D.G. HIGGINS, J. HERINGA, O. O'SULLIVAN, K SUHRE, C. ABERGEL License: Open source freeware
Tcoffee at a glance
Advantages and disadvantages of Tcoffee
T-Coffee stands for Tree based Consistency Objective Function for Alignment Evaluation. It is a recent program for making multiple sequence alignments. It yields more accurate alignments at the cost of a slightly longer running time than other programs. Although it uses a progressive alignment method like ClustalW, it compares segments across the entire sequence set, which means aligning all the sequences at the same time. The main difference between Tcoffee and ClustalW is that Tcoffee doesn’t directly use substitution matrices to align sequences. It has many different applications and modules such as the main EXPRESSO for aligning sequences and structures, CORE for evaluating the accuracy of an alignment, Mcoffee for combining many alternative multiple sequence alignments into one. Briefly, Tcoffee could be described as a collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA and protein sequences and structures.
Advantages
Tcoffee and its contribution to research Recently, many researchers in the field of molecular biology have used Tcoffee modules in building, computing, evaluating and manipulating multiple sequence alignments during their original research. Although Tcoffee has been produced and developed few years ago, it has been cited in many peer reviewed articles. However the number of citations is still not comparable to ClustalW. Beside its quick ability to produce results, the open source freeware license and its efficient multifunctional modules make Tcoffee one of the most useful programs for making multiple sequence alignments.
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It produces more accurate alignments than the other methods.
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It is equipped with many different tools and modules such as CORE, Mcoffee and EXPRESSO for structure alignment, evaluation and combining alignments.
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Tcoffee can deal with many input formats, including FASTA, Swiss-Prot and PIR (Protein Information Resource).
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Tcoffee produces sequence alignment in various formats so that it can be used as an input for another program. It also produces a colorized alignment where every residue appears on a background that indicates the quality of this alignment in (.html) and (.pdf) format.
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It can produce true phylogenetic tree in Newick format by using the Neighbor Joining method.
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It can work with list of DNA, RNA or protein sequences.
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Tcoffee can evaluate the quality of any multiple sequence alignments using CORE server.
Disadvantages -
It takes longer time to align multiple sequences than other programs.
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It has been cited in limited number of peer reviewed journals compared to ClustalW. However, this number is increasing rapidly every day.
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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.
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The data will remain available on the server for only nine days. Then it will be deleted.
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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, pp205217,2000. 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).
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/
New features, flavors and tools of Tcoffee Alignment TCOFFEE (Regular or advanced): Computes a multiple sequence alignment and the associated phylogenetic tree.
- http://www.ebi.ac.uk/t-coffee/ Ahmed MANSOUR Genetics Department, Faculty of Agriculture, Zagazig University, Egypt (author for correspondence;
[email protected]) Received: 27 March 2008; Accepted: 11 December 2009
