Algorithms in Bioinformatics (CSI 5126)
Review and presentation of a scientific paper — Fall 2010

Instructor: Lucia Moura

Version of October 12, 2010

1 Deadline

2 Objectives

3 Directives

Papers in (refereed) journals and conference proceedings are the main vehicles for communicating scientific information. November 2 (11:30-2:30) will be dedicated to the presentation of scientific publications in the field of exact and approximate string matching. The foundations 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. If you intend to propose a publication outside of the list, you must contact me by October 15 (E-mail me the details of the publications and a pdf, if available) and wait for my approval 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 motifs 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.

6 Evaluation criteria