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Grant support

Funding for open access charge: Plan Nacional (BFU2008-00419 to C.N. and P. D. T.); 7th Framework Programme of the European Commission, the LEISHDRUG (no 223414) and the Quantomics (KBBE-2A-222664) project; Computational resources are provided by the Center for Genomic Regulation (CRG) of Barcelona and the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the Swiss Institute of Bioinformatics; CUR of DIUE of GENCAT (to M.O. and A. M.); the Spanish ministry of education (TIN2008-05913); Consolider project (CSD 2007-00050);' Super-computacion y e-Ciencia (SYEC)'.

Analysis of institutional authors

Jia Ming, ChangAuthorTommaso, PAuthorNotredame CCorresponding Author

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March 25, 2020
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T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

Publicated to:Nucleic Acids Research. 39 W13-W17 - 2011-07-01 39(), DOI: 10.1093/nar/gkr245

Authors: Tommaso, P; Moretti, S; Xenarios, I; Orobitg, M; Montanyola, A; Chang, JM; Taly, JF; Notredame, C

Affiliations

Centre For Genomic Regulation (Pompeu Fabra University), Carrer del Doctor Aiguader 88, 08003 Barcelona, Spain. - Author
Pompeu Fabra Univ, Ctr Genom Regulat, Barcelona 08003, Spain - Author
Swiss Inst Bioinformat, Vital IT, CH-1015 Lausanne, Switzerland - Author
Univ Lausanne, Dept Ecol & Evolut Biophore, CH-1015 Lausanne, Switzerland - Author
Univ Lleida, Dept Comp Sci & Ind Engn, E-25001 Lleida, Spain - Author
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Abstract

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.

Keywords

AccuracyAlgorithmConsistencyHigh-throughputProgram

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal NUCLEIC ACIDS RESEARCH due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2011, it was in position 26/290, thus managing to position itself as a Q1 (Primer Cuartil), in the category Biochemistry & Molecular Biology.

From a relative perspective, and based on the normalized impact indicator calculated from the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 79.72, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: Dimensions Aug 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-08-08, the following number of citations:

  • WoS: 746
  • Scopus: 629
  • Europe PMC: 585

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-08-08:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 953.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 962 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 3.
  • The number of mentions on Wikipedia: 3 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Switzerland.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (di Tommaso, Paolo) and Last Author (Notredame, Cedric).

the author responsible for correspondence tasks has been Notredame, Cedric.