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

Nucleic acids research ·Vol. 32 ·No. Web Server issue ·2004-07-01 ·Pages W37-40

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

Abstract

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/.

MeSH Terms

Internet Proteins/chemistry Sequence Alignment Sequence Analysis, Protein Software

Chemicals

Proteins

Authors & Affiliations

5 authors, click to expand affiliations / ORCID

Poirot Olivier

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

Suhre Karsten

Abergel Chantal

O'Toole Eamonn

Notredame Cedric

References (17)

17 references, click to expand

T-Coffee: A novel method for fast and accurate multiple sequence alignment.
J Mol Biol. 2000 Sep 8;302(1):205-17 PMID: 10964570
Protein secondary structure prediction based on position-specific scoring matrices.
J Mol Biol. 1999 Sep 17;292(2):195-202 PMID: 10493868
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.
J Mol Biol. 2001 Jun 29;310(1):243-57 PMID: 11419950
HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families.
Bioinformatics. 2001 Aug;17(8):748-9 PMID: 11524380
Accounting for human polymorphisms predicted to affect protein function.
Genome Res. 2002 Mar;12(3):436-46 PMID: 11875032
Human non-synonymous SNPs: server and survey.
Nucleic Acids Res. 2002 Sep 1;30(17):3894-900 PMID: 12202775
The InterPro Database, 2003 brings increased coverage and new features.
Nucleic Acids Res. 2003 Jan 1;31(1):315-8 PMID: 12520011
ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins.
Nucleic Acids Res. 2003 Jul 1;31(13):3320-3 PMID: 12824317
Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments.
Nucleic Acids Res. 2003 Jul 1;31(13):3503-6 PMID: 12824354
APDB: a novel measure for benchmarking sequence alignment methods without reference alignments.
Bioinformatics. 2003;19 Suppl 1:i215-21 PMID: 12855461
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
Biopolymers. 1983 Dec;22(12):2577-637 PMID: 6667333
Protein structure alignment.
J Mol Biol. 1989 Jul 5;208(1):1-22 PMID: 2769748
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Nucleic Acids Res. 1994 Nov 11;22(22):4673-80 PMID: 7984417
The PROSITE database, its status in 1997.
Nucleic Acids Res. 1997 Jan 1;25(1):217-21 PMID: 9016539
COFFEE: an objective function for multiple sequence alignments.
Bioinformatics. 1998 Jun;14(5):407-22 PMID: 9682054
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs.
Bioinformatics. 1999 Jan;15(1):87-8 PMID: 10068696
Multiple sequence alignment in phylogenetic analysis.
Mol Phylogenet Evol. 2000 Sep;16(3):317-30 PMID: 10991785

Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

1362-4962

DOI

10.1093/nar/gkh382

Published

2004-07-01

Pages

W37-40

Language

English

Region

England

NLM ID

0411011

PMCID

PMC441520

Subset

External Links

PubMed source DOI: 10.1093/nar/gkh382 PMC Full Text View journal details

Analysis Services

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

Contact

WeChat Official Account