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BPS4104 Bioinformatics (Winter term)

Syllabus and textbook

Lab manual

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Weekly schedule:

Wk Chp Topic
1 1 Lec: String-matching algorithms in BLAST and FASTA
Lab: Sequence database and heuristic string matching: NCBI Entrez, BLAST and DAMBE
2 5, a, d Lec: Motif-characterizing algorithms
Lab: Position weight matrix and motif characterization
3 7, a, d Lec: Motif discovery with Gibbs sampler with optional EXCEL illustration
Lab: Gibbs Sampler and intron branchpoint sites (BPS)
4 c, i, m Lec: Lec: Introduction to RNA-Seq analysis
Lab: RNA-Seq software demonstration only (~1 hr)
5 8-9, b, f, j-l Lec: Amino acid and codon usage bias and indices
Lab: Codon Usage Bias
6 c, i, m Lec: Bioinformatics and translation initiation in prokaryotes and eukaryotes
1st mid-term exam+Lab: Secondary Structure, MFE And IRES
7 10, n Lec: Evolution of acid-resistance in Helicobacter pylori
Lab: Genomic Isoelectric Point Profiling
8 2 Lec: Molecular phylogeneitcs+Sequence alignment by dynammic programming
Lab: Sequence Alignment
9 13 Lec: Transition bias and substitution models
Lab: Choosing The Best-Fit Substitution Model
10 13 Lec: Distance-based methods
Lab: Molecular Phylogenetics
11 13, h Lec: Molecular clock
2nd mid-term exam+Lab: Testing The Molecular Clock Hypotheses
12 13, e Lec: Dating speciation and gene duplication events
Lab: Dating with the Least-Squares Method

Additional reading materials:

  1. Xia, X. 2012. Position Weight Matrix, Gibbs Sampler, and the Associated Significance Tests in Motif Characterization and Prediction. Scientifica, vol. 2012, Article ID 917540, 15 pages, 2012. doi:10.6064/2012/917540.
  2. Sun, X. Y., Yang, Q. Xia, X. 2012. An Improved Implementation of Effective Number of Codons (Nc). Molecular Biology and Evolution doi: 10.1093/molbev/mss201
  3. Xia, X. , MacKay, V., Yao, X., Wu, J., Miura, F. Ito, T. Morris, D. R. 2011. Translation initiation: a regulatory role for poly(A) tracts in front of the AUG codon in Saccharomyces cerevisiae. Genetics 189:469-478
  4. Ma, P.,Ma, P., Xia X. 2011. Factors affecting splicing strength of yeast genes. Comparative and Functional Genomics. Article ID 212146, 13 pages
  5. Xia, X. , Yang, Q. 2011. A Distance-based Least-square Method for Dating Speciation Events. Molecular Phylogenetics and Evolution 59:342-353.
  6. van Weringh, A, M. Ragonnet-Cronin, E. Pranckeviciene, M. Pavon-Eternod, L. Kleiman, X. Xia. 2011. HIV-1 modulates the tRNA pool to improve translation efficiency. Molecular Biology and Evolution 28:1827-1834
  7. Palidwor GA, Perkins TJ, Xia X. 2010. A General Model of Codon Bias Due to GC Mutational Bias. PLoS ONE 5(10): e13431.
  8. Xia, X. 2009. Information-theoretic indices and an approximate significance test for testing the molecular clock hypothesis with genetic distances. Molecular Phylogenetics and Evolution 52:665-676.
  9. Xia, X., Holcik, M., 2009. Strong Eukaryotic IRESs Have Weak Secondary Structure. PLoS ONE 4, e4136.
  10. Xia, X. 2008. The cost of wobble translation in fungal mitochondrial genomes: integration of two traditional hypotheses. BMC Evolutionary Biology 8:211.
  11. Carullo, M. and Xia, X. 2008 An extensive study of mutation and selection on the wobble nucleotide in tRNA anticodons in fungal mitochondrial genomes. Journal of Molecular Evolution 66:484-493 .
  12. Xia, X. 2007. An Improved Implementation of Codon Adaptation Index. Evolutionary Bioinformatics 3:53–58.
  13. Xia, X. 2007. The +4G site in Kozak consensus is not related to the efficiency of translation initiation. PLoS ONE 2(2):e188.
  14. Xia, X. and G. Palidwor. 2005. Genomic Adaptation to Acidic Environment: Evidence from Helicobacter pylori. American Naturalist 166:776-784
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