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Lectures by the
Computational Molecular
Biology Department at the
Max Planck Institute for
Molecular Genetics
Probability and Statistics for Sequence Analysis
Lecture+Exercise in WS 07/08
|
lecture |
exercise |
| Nr. |
19723 |
19723 |
| SWS |
2 |
2 |
| Credits |
3 |
3 |
| Time |
Wednesday, 10-12 |
Thursday, 14-16 |
| Place | Takusstr. 9, SR 051 |
MPI für Molekulare Genetik, Ihnestr. 73 |
| Schwerpunktbreich: |
C or D |
| Dozenten |
Martin Vingron
Utz J. Pape
|
| |
- 2nd January: Consider the updated lecture slots! No more tutorials!
- 25th October: Sorry, no exercise due to illness... Send me an eMail if you have any questions regarding the assignments!
- 18th October: Important material for the lecture is located here.
- 17th October: We do not have to change the room of the lecture. So, see you in SR 051 next week again
This course is intended for Master students, IMPRS students, students of Berlin School of Mathematics, and final year Bachelor students. The course discusses probability theory and statistics in sequence analysis for computational biologists (Bioinformatiker) and mathematicians. The two main topics are Alignment statistics (BLAST) and sequence patterns - their probability and derived statistics.
| Date |
Subject |
Lecturer |
Assignment |
| 17.10. |
Organization, Introduction to Probability and Statistics for Sequence Patterns
Single Word Counts for Permutation and Markov Models (Robin2005) |
Utz J. Pape |
none |
| 24.10. |
Single Word Counts
Dinucleotide Model (Robin2005) |
Utz J. Pape |
1 |
| 31.10. |
Single Word Counts
Expectation and Variance of Word Counts and Probability Basics (Robin2005) |
Utz J. Pape |
2 |
| 07.11. |
Single Word Counts
Exact Count Distribution, nth occurence, distance between two occurences, generating functions (Robin2005) |
Utz J. Pape |
3 |
| 14.11. |
Multiple Word Counts
Gaussian Approximation: Asymptotic expected value (Waterman1995) |
Utz J. Pape |
none |
| 21.11. |
Multiple Word Counts
Gaussian Approximation: Asymptotic Covariance (Waterman1995) |
Utz J. Pape |
4 |
| 28.11. |
Markov Chain Imbedding
(Fu1996) |
Hugues Richard |
5 |
| 05.12. |
Single Word Counts
Poisson Approximation and Compound Poisson Approximation (Robin2005, Waterman1995) |
Utz J. Pape |
6 |
| 12.12. |
Generating Functions for Single Words
Return probability, absence probability, waiting time, number of counts (Rahmann, chapter 5, 6, and 8) |
Utz J. Pape |
7 |
| 19.12. |
Generating Functions for Two Words
Return probability, absence probability, waiting time (Rahmann, chapter 7) |
Utz J. Pape |
none |
| 16.01. |
Probability and Statistics for Sequence Alignment: Head Runs |
Martin Vingron |
tba |
| 30.01. |
Probability and Statistics for Sequence Alignment |
Martin Vingron |
tba |
| 31.01. |
Probability and Statistics for Sequence Alignment |
Martin Vingron |
tba |
| 06.02. |
Probability and Statistics for Sequence Alignment |
Martin Vingron |
tba |
| 07.02. |
Probability and Statistics for Sequence Alignment |
Martin Vingron |
tba |
| 13.02. |
Probability and Statistics for Sequence Alignment |
Martin Vingron |
tba |
Go to the literature website to
find PDFs to read!
- Fu1996: Distribution theory of runs and patterns assciated with a sequence of multi-state trials from James C. Fu in Statistica Sinica (6) 1996.
- Rahmann: Word Statistics in Random Texts and Application to Computational Molecular Biology Diploma Thesis from Sven Rahmann, 2000.
- Regnier2000: A unified approach to word count probabilties from Mireille Regnier in Discrete Applied Mathematics, 2000
- Reinert2000: Probabilistic and statistical properties of words from Gesine Reinert, Sophie Schbath, and Michael Waterman in J Comput Biol, 2000
- Robin2005: DNA, Words and Models - Statistics of Exceptional Words from Stephane Robin, Francois Rodolphe, and Sophie Schbath, 2005
- Waterman1995: Introduction to Computational Biology - Maps, sequences and genomes from Michael Waterman, 1995
- oral or written exam at the end of the semester
- weekly assignments
- presence in lecture and exercise
Homepage der Abteilung Computational Molecular Biology am Max-Plack-Institut für Molekulare Genetik.
Zum Studiengang Bioinformatik an der FU Berlin.
Question, suggestions and remarks to Utz Pape. Last change: 09. July 2007 |
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