CSI5126. Algorithms in Bioinformatics
Review and presentation of a scientific paper — Fall 2017

Instructor: Marcel Turcotte

Version of October 3, 2017

[PDF]

1 Deadline

2 Learning outcomes

3 Directives

Papers in (refereed) journals and conference proceedings are the main vehicles for communicating scientific information. November 2 and 4 will be dedicated to the presentation of scientific publications in the field of exact and approximate string matching. The foundation of string matching algorithms has been presented in class, in the weeks preceding the presentations. You must select a publication that presents either a specialized application or a more efficient algorithm.

3.1 Deliverable

3.2 Selected publications

You must select a publication in a distinct area than that of your project. Below you will find a list of publications. You are welcomed to propose publications outside of the list. However, you must first contact me, E-mail me the details of the publication for instance, to make sure that your choice meets the didactic needs of the course.

Suitable topics include: software or hardware acceleration of the sequence alignment problem, heuristics for accelerating alignment methods, improved substitutions or gap models, repeat finding methods, including tandem repeats. Avoid subjects such as motif detections, which in general involves coupling approximate matching algorithms with statistical inference tools — we will specifically visit these topics toward the end of the semester.

4 Resources

5 Frequently Asked Questions (FAQ)

  1. None, yet.

6 Evaluation criteria

The evaluation is as follows: my evaluation of your presentation (80%), evaluation the presentation by your peers (10%), summary of the publication (10 %).

PIC