XiaLab at University of Ottawa

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BPS4104/BIO8102H Bioinformatics (Winter term)

Student composition: Biochem (9.80%), Biology (3.92%), BioMed (7.84%), BioPharm (76.47%), Geology (1.96%).

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

Weekly lecture/lab schedule (Voice-over slides will be uploaded to Brightspace):

DateChpTopic
2021-1-10 1Lec: String-matching algorithms in BLAST and FASTA
Lab: Sequence database and heuristic string matching: NCBI Entrez, BLAST and DAMBE
2021-1-17 3Lec: Motif-characterizing algorithms
Lab: Position weight matrix and motif characterization
2021-1-24 4Lec: Motif discovery with Gibbs sampler with optional EXCEL illustration
Lab: Gibbs Sampler and intron branchpoint sites (BPS)
2021-1-31 5Lec: Lec: Introduction to RNA-Seq analysis
Lab: RNA-Seq software demonstration only (~1 hr)
2021-2-7 9Lec: Amino acid and codon usage bias and indices
1st mid-term exam+Lab: Codon Usage Bias
2021-2-14  Reading week
Reading week
2021-2-21 8Lec: Bioinformatics and translation initiation
Lab: Secondary Structure, MFE And IRES
2021-2-28 17Lec: Evolution of acid-resistance in Helicobacter pylori
Lab: Genomic Isoelectric Point Profiling
2021-3-7 2Lec: Sequence alignment by dynammic programming
Lab: Sequence Alignment
2021-3-14 12Lec: Transition bias and substitution models
Lab: Choosing The Best-Fit Substitution Model
2021-3-21 14-16Lec: Molecular phylogenetics
Mar. 22, 2nd mid-term exam+Lab: Molecular Phylogenetics
2021-3-28 15-16Lec: Molecular clock
Lab: Testing The Molecular Clock Hypotheses
2021-4-4 15Lec: Dating speciation and gene duplication events
Lab: Dating with the Least-Squares Method
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