Figure 1

Web Interface Scheme. NemaFootPrinter scheme: starting from gene name submission ('Start analysis' on the top-left of the scheme), gene name and organism are submitted to the GENEFINDER script (red-border box) that verifies if the given gene has an ortholog and displays the clone name. GENEFINDER also allows not-interactive selection of n base pairs upstream and downstream of the given genes. After gene-name retrieval the user can choose a display mode (green-border boxes): TEXT-MODE allows non-interactive selection of subsequences; the SLIDER-MODE uses an Applet Java to select interactively sub-sequences; the FRAME-MODE combines the slider and the result page on two horizontal frames. On the RESULTS page (blue-border boxes) users can find images of genes structure and boundaries generated on the fly, links to the sequences (FASTA format) and links to a series of bioinformatics tools (yellow-border boxes): BLAST 2 sequences is used for a first screening of the two sequences for similarities; Dotmatcher generates a dot plot and associate an image for direct graphical visualization of regions of similarity. By clicking on a point into the Dotmatcher image and extending the selection for n base pairs, it is possible to align small regions with the Smith and Waterman algorithm. One can then send Fasta files and Blastz alignments to the rVista server (the two subsequences and the relative Blastz alignment generated on the local server). Through this public database it is possible to identify the transcriptional regulatory elements, if any, associated with conserved subsequences.