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Bioinformatics Vol. 17 no. 7 2001
Pages 656-657
© 2001 Oxford University Press

Applications Note

MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs

Raf M. Podowski and Erik L. L. Sonnhammer

Center for Genomics Research, Karolinska Institutet, S-171 77 Stockholm, Sweden

Received on January 12, 2001 ; revised on March 14, 2001 ; accepted on March 16, 2001

Summary: MEDUSA is a tool for automatic selection and visual assessment of PCR primer pairs, developed to assist large scale gene expression analysis projects. The system allows specification of constraints of the location and distances between the primers in a pair. For instance, primers in coding, non-coding, exon/intron-spanning regions might be selected. Medusa applies these constraints as a filter to primers predicted by three external programs, and displays the resulting primer pairs graphically in the Blixem (Sonnhammer and Durbin, Comput. Appl. Biosci. 10, 301–307, 1994; http://www.cgr.ki.se/cgr/groups/sonnhammer/Blixem.html) viewer.

Availability: The MEDUSA web server is available at http://www.cgr.ki.se/cgr/MEDUSA. The source code and user information are available at ftp://ftp.cgr.ki.se/pub/prog/medusa.

Contact: Erik.Sonnhammer{at}cgr.ki.se


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