Vito, a Tool for Refinement of Protein Sequence-structure Alignments. Introduction

Summary: ViTO is a graphical application including an editor of multiple sequence alignment and a 3D structure viewer. It is possible to manipulate alignments containing hundreds of sequences and to display a dozen of 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 immediat 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/ Contact: [email protected], [email protected] Supplementary information : http://bioserv.cbs.cnrs.fr/VITO/DOC/index.html