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Nucleic Acids Research 2005 33(Web Server Issue):W289-W294; doi:10.1093/nar/gki390
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information

V. A. Simossis1 and J. Heringa1,2,*

1Bioinformatics Section, Faculty of Sciences, Vrije Universiteit De Boelelaan 1081A, 1081 HV, Amsterdam, The Netherlands 2Centre for Integrative Bioinformatics VU (IBIVU), Faculty of Sciences and Faculty of Earth & Life Sciences, Vrije Universiteit De Boelelaan 1081A, 1081 HV, Amsterdam, The Netherlands

*To whom correspondence should be addressed. Tel: +31 20 5987649; Fax: +31 20 5987653; Email: heringa{at}cs.vu.nl

Received February 11, 2005. Revised March 10, 2005. Accepted March 10, 2005.

PRofile ALIgNEment (PRALINE) is a fully customizable multiple sequence alignment application. In addition to a number of available alignment strategies, PRALINE can integrate information from database homology searches to generate a homology-extended multiple alignment. PRALINE also provides a choice of seven different secondary structure prediction programs that can be used individually or in combination as a consensus for integrating structural information into the alignment process. The program can be used through two separate interfaces: one has been designed to cater to more advanced needs of researchers in the field, and the other for standard construction of high confidence alignments. The web-based output is designed to facilitate the comprehensive visualization of the generated alignments by means of five default colour schemes based on: residue type, position conservation, position reliability, residue hydrophobicity and secondary structure, depending on the options set. A user can also define a custom colour scheme by selecting which colour will represent one or more amino acids in the alignment. All generated alignments are also made available in the PDF format for easy figure generation for publications. The grouping of sequences, on which the alignment is based, can also be visualized as a dendrogram. PRALINE is available at http://ibivu.cs.vu.nl/programs/pralinewww/.


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