Section: New Software and Platforms
Iedera : subset seed design tool
Keywords: Computational biology - Sequence alignment - Spaced seeds
Iedera is a tool based on a weighted automata framework that enables to compute spaced seeds, associated probability distributions, scores/costs, counts, and even polynomials on a classical semi-ring framework. Seed design is computed by full enumeration or hill-climbing optimization.
Iedera is a tool to select and design subset seed and vectorized subset seed patterns. Spaced seeds and transition-constrained spaced seeds can be perfectly represented in the subset seed model.