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PMID: 16845081 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Nucleic acids research ·Vol. 34 ·No. Web Server issue ·2006-07-01 ·Pages W604-8

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

Abstract

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/.

MeSH Terms
Databases, Protein Internet Protein Conformation Sequence Alignment/methods Software User-Computer Interface
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Armougom Fabrice
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.
Moretti Sébastien
Poirot Olivier
Audic Stéphane
Dumas Pierre
Schaeli Basile
Keduas Vladimir
Notredame Cedric
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkl092
Published
2006-07-01
Pages
W604-8
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1538866
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkl092 PMC Full Text View journal details
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