Day 1 – November 21, 2016
- Exercise: Multiple Sequence Alignment and Analysis (PDF)
- Exercise: Multiple Sequence Alignment and Analysis (ODT)
Handouts: nbic-phd-course-comp-genomics-day1-af4-handout_shrunk
Literature:
- Multi-Harmony: detecting functional specificity from sequence alignment (Berndt Brand)
- Sequence comparison by sequence harmony identifies subtype-specific functional sites (Walter Pirovano)
Zipfile with reference sequence sets
Day 2 – November 22, 2016
Handouts/lectures:
Day 3 – November 23, 2016
Lecture Jaap Heringa: biosb-phd-course-comp-genomics-2016-day3-jh
- Practical assignment: compgenomics_2016_day3_biological_networks_practical
- Answers: compgenomics_2016_day3_short_answers_biological_networks_practical
Lecture Martijn Huynen (Bayesian): bayesian-integration-simple
- question-bayesian-integration
- ciliacarta_table_for_students_negative_set
- ciliacarta_table_for_students_positive_set
- ciliacarta_table_for_students_candidates
Day 4 – November 24, 2016
Lecture/slides Berend Snel:
- http://bioinformatics.bio.uu.nl/snel/BEG/BioSB_tree_reconciliation.pdf
- http://bioinformatics.bio.uu.nl/snel/BEG/WGD_2016.pdf
Exercises:
- http://bioinformatics.bio.uu.
nl/snel/BEG/exercises_WGD.html - http://www-binf.bio.uu.nl/
snel/BEG/exercise_peroxisome. html - http://www-binf.bio.uu.nl/snel/BEG/exercise_RPL22.html
Day 5 – November 25, 2016
Lectures/slides Martijn Huynen:
Exercises:
Literature:
- Positive Selection of Tyrosine Loss in Metazoan Evolution
- Comment on “Positive Selection of Tyrosine Loss in Metazoan Evolution”
- Response to Comment on “Positive Selection of Tyrosine Loss in Metazoan Evolution”