Introduction to Statistical and Computational Genomics

GENOME 559
Department of Genome Sciences
University of Washington
Winter Quarter


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Class schedule

Date            Lecture Topic Programming Topic Reading Homework
Assigned
Tue Jan 8 Course overview. Intro to sequence comparison Introduction to Python (Unix reference) Chapters 1-2  
Thu Jan 10 Sequence comparison — dynamic programming Strings Chapter 8 Homework 1
Tue Jan 15 Sequence comparison — traceback Numbers, lists and tuples Chapters 10, 12  
Thu Jan 17 Sequence comparison — local alignment File I/O Chapter 14 Homework 2
Tue Jan 22 Significance of similarity scores Conditionals Chapter 5  
Thu Jan 24 Multiple testing correction For loops (matrix.txt) Chapter 7 Homework 3 (red green yellow blue)
Tue Jan 29 Motif search More for loops (sample.fa)    
Thu Jan 31 Motif p-values compute-motif-pvalue.py int-motif.txt my-pssm.txt   Homework 4 kmer_input_seq.txt CRISPR_seq.fastq
Tue Feb 4 FDR control pvalues.txt While loops   (Noble 2009)  
Thu Feb 6 Motif discovery Dictionaries small-scores.txt large-scores.txt unique-scores.txt seq-names.txt (D'haeseleer 2006) Homework 5 decode_seq_signal.py example_chromosome21.txt for_loop_to_while_loop.py seq_errors.fastq
The remainder of the lecture schedule will be posted soon.
Mon Mar 16
Final exam, 10:30 am - 12:20 pm, Foege S040