Abstract Summary: Analyzing and visualizing multiple sequence alignments is a common task in many areas of molecular biology and bioinformatics. Many tools exist for this purpose, but are not easily customizable for specific in-house uses. Here we report the development of an editor, CINEMA-MX, that addresses these issues. CINEMA-MX is highly modular and configurable, and we present examples to illustrate its extensibility. Availability: The program and full source code, which are available from http://www.bioinf.man.ac.uk/dbbrowser/cinema-mx, are being released under a combination of the LGPL and GPL, for Unix or Windows platforms. Contact: [email protected] * To whom correspondence should be addressed at Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK

Abstract Summary: With the ever-increasing need to handle large volumes of sequence data efficiently and reliably, we have developed the EASY system for performing combined protein sequence and pattern database searches. EASY runs searches simultaneously and distils results into a concise 1-line diagnosis. By bringing together results of several different analyses, EASY provides a rapid means of evaluating biological significance, minimising the risk of inferring false relationships, for example from relying exclusively on top BLAST hits. The program has been tested using a variety of protein families and was instrumental in resolving family assignments in a major update of the PRINTS database. Availability: http://www.bioinf.man.ac.uk/dbbrowser/easy/ Contact: [email protected] * To whom correspondence should be addressed.