Nucleic Acids Research, 2005, Vol. 33, Web Server issue W541 Figure 1. The input window (A) allows users to control most YASS parameters, from most basic to more advanced. Results are output in tabular format (B), with the possibility of displaying each sequence alignment (C). Once the results are obtained, it is possible to generate a clickable dot-plot (Figure 2) where each alignment is linked to a URL with its text representation (Figure 1C). A tabular output (Figure 1B) is also available: alignments are sorted according to their E-value and linked to their text representation. Finally, the YASS output can also be down- loaded in text format for further analysis. Technical issues. The YASS server available at http:// yass.loria.fr/interface.php currently runs Apache 2.0.47