XiaLab at University of Ottawa

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BPS4104/BIO8102H Bioinformatics (Winter term)

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


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


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

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

2023-1-091Lec: String-matching algorithms in BLAST and FASTA
Lab: Sequence database and heuristic string matching: NCBI Entrez, BLAST and DAMBE
2023-1-163Lec: Motif-characterizing algorithms
Lab: Position weight matrix and motif characterization
2021-1-254Lec: Motif discovery with Gibbs sampler with optional EXCEL illustration
Lab: Gibbs Sampler and intron branchpoint sites (BPS)
2021-2-15Lec: Lec: Introduction to RNA-Seq analysis
Lab: RNA-Seq software demonstration only (~1.5 hr, PPT)
2021-2-83Lec: Amino acid and codon usage bias and indices
1st mid-term exam+Lab: Codon Usage Bias
2021-2-223Lec: Bioinformatics and translation initiation
Lab: Secondary Structure, MFE And IRES
2021-2-153Reading week
Reading week
2021-3-13Lec: Evolution of acid-resistance in Helicobacter pylori
Lab: Genomic Isoelectric Point Profiling
2021-3-83Lec: Sequence alignment by dynammic programming
Lab: Sequence Alignment
2021-3-153Lec: Transition bias and substitution models and EXCEL file for practice
Lab: Choosing The Best-Fit Substitution Model
2021-3-223Lec: Molecular phylogenetics
Mar. 22, 2nd mid-term exam+Lab: Molecular Phylogenetics
2021-3-293Lec: Molecular clock
Lab: Testing The Molecular Clock Hypotheses
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