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1: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W37-40.Click here to read Click here to read Links

3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment.

Poirot O, Suhre K, Abergel C, O'Toole E, Notredame C.

Information Génomique et Structurale UPR2589-CNRS, CNRS, 31, Chemin Joseph Aiguier, 13 402 Marseille Cedex 20, France.

This paper presents 3DCoffee@igs, a web-based tool dedicated to the computation of high-quality multiple sequence alignments (MSAs). 3D-Coffee makes it possible to mix protein sequences and structures in order to increase the accuracy of the alignments. Structures can be either provided as PDB identifiers or directly uploaded into the server. Given a set of sequences and structures, pairs of structures are aligned with SAP while sequence-structure pairs are aligned with Fugue. The resulting collection of pairwise alignments is then combined into an MSA with the T-Coffee algorithm. The server and its documentation are available from http://igs-server.cnrs-mrs.fr/Tcoffee/.

PMID: 15215345 [PubMed - indexed for MEDLINE]

PMCID: PMC441520

2: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W604-8.Click here to read Click here to read Links

Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee.

Armougom F, Moretti S, Poirot O, Audic S, Dumas P, Schaeli B, Keduas V, Notredame C.

Laboratoire Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 Avenue de Luminy, FR- 13288, Marseille cedex 09, France.

Expresso is a multiple sequence alignment server that aligns sequences using structural information. The user only needs to provide sequences. The server runs BLAST to identify close homologues of the sequences within the PDB database. These PDB structures are used as templates to guide the alignment of the original sequences using structure-based sequence alignment methods like SAP or Fugue. The final result is a multiple sequence alignment of the original sequences based on the structural information of the templates. An advanced mode makes it possible to either upload private structures or specify which PDB templates should be used to model each sequence. Providing the suitable structural information is available, Expresso delivers sequence alignments with accuracy comparable with structure-based alignments. The server is available on http://www.tcoffee.org/.

PMID: 16845081 [PubMed - indexed for MEDLINE]

PMCID: PMC1538866

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