Skip Navigation


Nucleic Acids Research Advance Access originally published online on April 22, 2007
Nucleic Acids Research 2007 35(Web Server issue):W649-W652; doi:10.1093/nar/gkm227
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1895K) Freely available
Right arrow Screen PDF (240K) Freely available
Right arrowOA All Versions of this Article:
35/suppl_2/W649    most recent
gkm227v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Pei, J.
Right arrow Articles by Grishin, N. V.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Pei, J.
Right arrow Articles by Grishin, N. V.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W649-W652
© 2007 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

PROMALS web server for accurate multiple protein sequence alignments

Jimin Pei1,*, Bong-Hyun Kim2, 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, Texas 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, 2007. Revised March 22, 2007. Accepted March 28, 2007.

Multiple sequence alignments are essential in homology inference, structure modeling, functional prediction and phylogenetic analysis. We developed a web server that constructs multiple protein sequence alignments using PROMALS, a progressive method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS shows higher alignment accuracy than other advanced methods, such as MUMMALS, ProbCons, MAFFT and SPEM. The PROMALS web server takes FASTA format protein sequences as input. The output includes a colored alignment augmented with information about sequence grouping, predicted secondary structures and positional conservation. The PROMALS web server is available at: http://prodata.swmed.edu/promals/


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.