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Nucleic Acids Research Advance Access originally published online on May 24, 2008
Nucleic Acids Research 2008 36(Web Server issue):W30-W34; doi:10.1093/nar/gkn322
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W30-W34
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

PROMALS3D web server for accurate multiple protein sequence and structure alignments

Jimin Pei1,*, Ming Tang1 and Nick V. Grishin1,2

1Howard Hughes Medical Institute and 2Department of Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9050, USA

*To whom correspondence should be addressed. Tel: +214 645 5951; Fax: +214 645 5948; Email: jpei{at}chop.swmed.edu

Received January 31, 2008. Revised April 24, 2008. Accepted May 7, 2008.

Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/.


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