medusa

medusa automates selection and visual assessment of PCR primer pairs for large-scale gene expression analysis.

Key Features:

• Automated Primer Selection: Applies predefined constraints on primer location and spacing within DNA sequences to select PCR primer pairs for coding regions, non-coding sequences, or exon/intron‑spanning targets.
• Constraint-Based Filtering: Filters candidate primers using user-specified parameters and applies those filters to primers predicted by three external programs.
• Graphical Visualization: Displays resulting primer pairs using the Blixem viewer (Sonnhammer and Durbin, COMPUT: Appl. Biosci. 10, 301-307, 1994) for visual assessment.

Scientific Applications:

• Large-scale gene expression studies: Supports selection of primer pairs for high-throughput PCR experiments requiring consistent primer placement and spacing.
• Targeted primer design: Enables design and assessment of primers targeting coding regions, non-coding sequences, or exon–intron boundaries.

Methodology:

Integrates primer predictions from three external programs with user-defined location and spacing constraints to filter and refine primer candidates and presents results via the Blixem viewer.