Page AdvancedAlgorithms11

Welcome to the Wiki of the Lecture Advanced Algorithms in Bioinformatics (P4).

News

Exam Results

Mat Pts Grade
xxx4940 62,5 2,0
xxx1192 27 5,0
xxx0760 0 5,0
xxx9983 0 5,0
xxx2042 45 3,3
xxx2152 49 3,0
xxx1288 0 5,0
xxx4523 0 5,0
xxx0284 39 3,7
xxx2000 71 1,3
xxx2779 0 5,0
xxx6890 62,5 2,0
xxx6034 39 3,7
xxx1235 65 1,7
xxx9546 68 1,3
xxx9672 57 2,3
xxx9469 43 3,3
xxx2200 43,5 3,3
xxx4248 43 3,3

Schedule

Event Day Time Address Room
Lecture Mon 14-16 Arnimallee 14 SR FB (1.1.16)
Lecture Fri 14-16 Takustr. 9 006
Exercise Wed 14-16 Takustr. 9 006

Date Lecture Block Lecturer
11.04.-06.05. Online String Searching and Filtering David Weese
09.05.-30.05. Index Data Structures David Weese
11.05. Review 1  
03.06.-17.06. Genome Comparison and RNA Analysis Sandro Andreotti
08.06. Review 2  
29.06. Klausur  
18.06.-16.07. Individual Projects  

Exercises

You can download the exercise sheets on the subpages of the different lecture blocks.

Reviews

Requirements for Aktive Teilnahme

You have to hand in 75% of all exercise problems. (An exercise problem counts, if it is clearly visible that a solution was attempted for some time.) In addition you need to reach 50% of all points of the two reviews.

Projects

The time from 18.06. to 16.07. is reserved for your projects. Please pick a project from below and sign in on this (coming soon) page. You are expected to write a C++ program which you have to successfully present and explain in a code review.

For additional information and material check: P4Projects

Project A: Suffix array search (Firdevs, Hatice)

Project B: FM-Index (Arthur, Felix, Duc)

Project C: Pigeonhole Filter (Aileen, Anke, Yvonne)
Implement the hierarchical filter (PEX) to find approximate matches of a pattern with up to k edit-errors in a text.

Project D: QUASAR (Daniel, Jörn)
Implement QUASAR to search semi-global alignments with up to k edit-errors of patterns in a text.

Project E: Calculation of the exact q-gram threshold (Franzi, Christopher)

Project F: Skew algorithm (Mathias, Oliver, Jan-Martin)
Implement the skew-algorithm for the difference cover D = {1,2,4} and m = 7

Project G: Nussinov SCFG (Martin, Kurt)

References

Please note that some journals might only be accessible from granted subnets like the FU subnet (or VPN).

[1] Stefan Burkhardt, Juha Kärkkäinen, Better Filtering with Gapped q-Grams, Fundamenta Informaticae, 2003
[2] http://en.wikipedia.org/wiki/Maximum_coverage_problem