Section: New Software and Platforms

Iedera

Iedera : subset seed design tool

Keywords: Computational biology - Sequence alignment - Spaced seeds

Scientific Description

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.

Functional Description

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.

• Participants: Laurent Noé, Grégory Kucherov and Mikhail Roytberg

• Partners: CNRS - Université de Nancy - Université de Lille

• Contact: Laurent Noé

• URL: http://bioinfo.lifl.fr/yass/iedera.php