Page ProgressReportSiragusaFall2010

Accomplishments up to the Fall 2010

• Familiarized with SeqAn.
• Read most of the literature on seed design.

Goals for the Fall 2010

Literature

Reading

• Finish reading seed design literature including Noe and Burkhardt PhD Thesis.
• Read motif finding literature including Lim Master Thesis.

Writing

• Write an essay on the state of the art of seed design. A current version can be found here.

Research

Seed Properties Computation

• Prove a PTAS for the threshold T_F(m,k).
• Extend the T_F(m,k) greedy algorithm to compute undetected U_F(m,k) and single detected S_F(m,k,l) similarities.

Search Space Analysis

• Find bounding criteria for single seeds, like U' contained in U implies T_U'(m,k) gte T_U(m,k).
• Evaluate PatternHunterII greedy method for seed families.
• Propose alternative heuristics.

Model Design

• Conceive a framework for seed design optimizing a seed family w.r.t. specificity for a given sensitivity threshold.

Motif Finding

• Conceive a motif finder based on the seed design framework.

SeqAn

Development

• Prototype a seed design module.

Maintenance

• Familiarize with motif finding module.
• Fix motif finding module.

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