You are here:
Foswiki
>
ABI Web
>
ResearchLogEnricoSiragusa
>
ProgressReportSiragusaFall2010
(07 Dec 2010, EnricoSiragusa)
Edit
Attach
Page
ProgressReportSiragusaFall2010
This is the progress report of Enrico Siragusa for the Fall 2010.
Accomplishments up to the Fall 2010
Goals for the Fall 2010
Literature
Reading
Writing
Research
Seed Properties Computation
Search Space Analysis
Model Design
Motif Finding
SeqAn
Development
Maintenance
Comments
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.
Comments
E
dit
|
A
ttach
|
P
rint version
|
H
istory
: r6
<
r5
<
r4
<
r3
|
B
acklinks
|
V
iew wiki text
|
Edit
w
iki text
|
M
ore topic actions
Topic revision: r5 - 07 Dec 2010, EnricoSiragusa
- This page was cached on 28 Apr 2025 - 12:06.
ABI
ABI Library
Consultations Knut Reinert
Contact
Events, Conferences, Talks
Members
Projects
Publications
Teaching
Theses
Wiki
Copyright © by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding Foswiki?
Send feedback