Abstract Summary: Prophinder is a prophage prediction tool coupled with a prediction database, a web server and web service. Predicted prophages will help to fill the gaps in the current sparse phage sequence space, which should cover an estimated 100 million species. Systematic and reliable predictions will enable further studies of prophages contribution to the bacteriophage gene pool and to better understand gene shuffling between prophages and phages infecting the same host. Availability: Softare is available at http://aclame.ulb.ac.be/prophinder Contact: [email protected] Supplementary information: Supplementary data is available on http://aclame.ulb.ac.be/Tools/Prophinder/evaluations_table.html.

Abstract Summary: MaxBench is a web-based system available for evaluating the results of sequence and structure comparison methods, based on the SCOP protein domain classification. The system makes it easy for developers to both compare the overall performance of their methods to standard algorithms and investigate the results of individual comparisons. Availability: http://www.sanger.ac.uk/Users/lp1/MaxBench/ Contact: [email protected] * To whom correspondence should be addressed.