Bioinformatics Advance Access originally published online on July 22, 2004
Bioinformatics 2004 20(18):3694-3696; doi:10.1093/bioinformatics/bth429
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Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.
Applications Note |
ViTO: tool for refinement of protein sequence–structure alignments
Centre de Biochimie Structurale, INSERM U414, CNRS UMR5048, Université Montpellier 1 15, Avenue Charles Flahault 34060 Montpellier Cedex, France
Received on June 3, 2004; revised on July 7, 2004; accepted on July 17, 2004
Advance Access Publication July 22, 2004
Summary: ViTO is a graphical application, including an editor, of multiple sequence alignment and a three-dimensional (3D) structure viewer. It is possible to manipulate alignments containing hundreds of sequences and to display a dozen structures. ViTO can handle so-called ‘multiparts’ alignments to allow the visualization of complex structures (multi-chain proteins and/or small molecules and DNA) and the editing of the corresponding alignment. The 3D viewer and the alignment editor are connected together allowing rapid refinement of sequence–structure alignment by taking advantage of the immediate visualization of resulting insertions/deletions and strict conservations in their structural context. More generally, it allows the mapping of informations about the sequence conservation extracted from the alignment onto the 3D structures in a dynamic way. ViTO is also connected to two comparative modelling programs, SCWRL and MODELLER.
These features make ViTO a powerful tool to characterize protein families and to optimize the alignments for comparative modelling.
Availability: http://bioserv.cbs.cnrs.fr/VITO/DOC/
Supplementary information: http://bioserv.cbs.cnrs.fr/VITO/DOC/index.html
Contact: catrino{at}cbs.cnrs.fr
* To whom correspondence should be addressed.
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