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BPS4104/BIO8102H Bioinformatics (Winter term)

Student composition: BioPharm (78.13%), Biochem (15.63%), BioMed (5.00%), Other (1.24%).

Syllabus

Textbook: Xia, X. 2018. Bioinformatics and the cell: Modern computational approaches in genomics, proteomics and transcriptomics. 2nd edition. (You can download the book free using a campus PC or purchase a hard copy for $24.99.)

Lab manual in PDF format

Download zone

The mid-term exam files will be ready for downloading at the scheduled exam time. The URL of the exam files is

http://dambe.bio.uottawa.ca/teach/bps4104_download/WhatExam/########.xlsx

(where "WhatExam" is either "Midterm1", "Midterm2" or "Final", and "########" is your student ID)

Weekly lecture/lab schedule (This is generic. Access Brightspace for updated schedule and lecture slides)

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WeekChpTopic
11Lec: String-matching algorithms in BLAST and FASTA
Lab: Sequence database and heuristic string matching: NCBI Entrez, BLAST and DAMBE
23Lec: Motif-characterizing algorithms
Lab: Position weight matrix and motif characterization
34Lec: Motif discovery with Gibbs sampler with optional EXCEL illustration
Lab: Gibbs Sampler and intron branchpoint sites (BPS)
45Lec: Lec: Introduction to RNA-Seq analysis
Lab: RNA-Seq software demonstration only (~1.5 hr, PPT)
53Lec: Amino acid and codon usage bias and indices
1st mid-term exam+Lab: Codon Usage Bias
63Lec: Bioinformatics and translation initiation
Lab: Secondary Structure, MFE And IRES
73Lec: Evolution of acid-resistance in Helicobacter pylori
Lab: Genomic Isoelectric Point Profiling
83Lec: Sequence alignment by dynammic programming
Lab: Sequence Alignment
93Lec: Transition bias and substitution models and EXCEL file for practice
Lab: Choosing The Best-Fit Substitution Model
103Lec: Molecular phylogenetics
Mar. 22, 2nd mid-term exam+Lab: Molecular Phylogenetics
113Lec: Molecular clock
Lab: Testing The Molecular Clock Hypotheses
123Lec: Dating speciation and gene duplication events
Term-end quiz (FindHomologue) + Lab: Dating with the Least-Squares Method
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