Alignment visualization tools

Hanke, J. Reich, J. G. (1996). Kohonen map as a visualization tool for the analysis of protein sequences multiple alignments, domains and segments of secondary structures. Comput Applic Biosci 6,447-54. 

Shah, N Couronne, O., Pennacchio, L. A., et al. (2004) PhyloVISTA an interactive visualization tool for multiple DNASequence alignments. Bioinformatics 20, 636-643. 

Ovcharenko, I., Loots, G. G Hardison, R. C., Miller, W., and Stubbs, L. (2004) zPicture dynamic alignment and visualization tool for analyzing conservation profiles. Genome Res. 14, 472-477. 

Bus for gene prediction and multiple sequence alignment, along with visualization tools ... 

Hanke and Reich used Kohonen nets as a visualization tool for the analysis of protein sequence similarity (ISO). The proeedure eonverts sequenee (domains, aligned sequences, and segments of seeondary strueture) into a ehar-acteristie signal matrix. This eonversion depends on the property or replaee-ment seore vector selected by the user. The trained Kohonen network is functionally equivalent to an unsupervised nonlinear eluster analyzer. Protein families, or aligned sequences, or segments of similar seeondary strueture aggregate as clusters and their proximity may be inspeeted. 

Another class of 3D descriptors is molecular interaction field (MIF) descriptors, with its well-known example of Comparative Molecular Field Analysis (204,205) (CoMFA). In CoMFA, the steric and electrostatic fields are calculated for each molecule by interaction with a probe atom at a series of grid points surrounding the aligned molecules in 3D space. These interaction energy fields are correlated with the property of interest. The 3D nature of the CoMFA technique provides a convenient tool for visualization of the significant features of the resulting models. 

The ExPASy server (www.expasy.chl is one of the most useful servers, where almost any bioinforma tic tool can be found, together with useful links to other websites such as NCBI or EBI. The several access databases are descriptive, easy to follow, and up to date. Protein data bank searches with SwissProt or Trembl, as well as sequence alignments using either SimAlign (for two sequences) or ClustalW (for more than two protein sequences) can be started from ExPASy, to name just a few of the possibilities available. Access is also given to the Roche Applied Science Biochemical pathways where either keyword searches for particular enzymes or for metabolites can be performed, or entire metabolic pathways or sections thereof can be visualized. Proteomics evaluation is also available on ExPASy, which features free 2D-PAGE software called Melanie. 

Chemometric techniques can be valuable tools for the exploration of CE data as well as for the classihcation of samples based on electrophoretic data. The techniques maximally exploit the multivariate character of the data. In several applications, it was demonstrated that chemometric approaches can extract more information from electropherograms than only a visual inspection can. It is very important, especially when using entire electropherograms, that the CE data are preprocessed (e.g., aligned) in an appropriate way prior to other chemometric calculations, because CE analyses generally exhibit a rather poor reproducibility. 

Similar to Prompt, AlViz [Lanzenberger and Sampson 2006] is a plugin for Protege, however the tool is primarily in an early research phase. AlViz was developed specifically for visualizing ontology alignments. It applies multiple-views... 

VISTA presentation of comparative data is easy to interpret both on a small and a large scale, i.e., at different levels of resolution. All VISTA programs and servers use the same type of visualization, making interpretation of alignments easy. Because VISTA tools are being constantly improved and enhanced, new options and capabilities can be found on the website. The VISTA support group (vista lbl.gov) will help users explore these new options and answer questions. 

A summary page will comprehensively display the results of the TFBS analysis (Fig. 8C). Flere, users can access position and matrix information provided for each sequence independently, as well as the sites can be visualized on top of the alignment and used in subsequent clustering analysis (Figs. 8C and 9A). The clustering options are similar to the ones available for the rVISTA 2.0 tool, TFBS can be clustered individually or combinatorially and the sites can be visualized... 

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