An extremely difficult research assignment. It combines a research on advanced automata-based pattern matching with advanced technology of gene annotations. The assignment is even more difficult due to the supervisor's illiteracy in gene annotation and computational biology. It is also very ambitious, aiming at outperforming state-of-the-art tools in gene annotation. 

This project has been going on for several years, starting by an experimental collaboration and slowly evolving into a serious research endevour with a high potential to generate publications. Most of the credit for this goes to the student, who compensated for my lack of knowledge in computational biology, carried on with tenacity even after major setbacks (we run into several dead ends on the way, for instance with the Alergia learning approach), solved technical problems, understood quickly her advisor's half baked ideas and turned them into meaningful conversations and later solutions, and came up with very good and fresh ideas by herself. She has shown an exceptional abilities in theory and algorithm design as well as in implementation. The amount of work actually exceeds an excellent diploma thesis. 

The work is almost ready for publication, it may even turn into a research direction.  

Stupeň hodnocení: obtížnější zadání

I find the assignment quite difficult, as it required the student to study advanced methods of biological sequence alignment along with related topics in automata theory.

The report is written in solid English, with only very minor problems.

I think that the work could lead to a publication.

Stupeň hodnocení: přesahuje obvyklé rozmezí

Even though the thesis is longer than usual, it contains no unnecessary information. The length is justified and reflects the substantial amount of work the student has completed.