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BPS4104 Bioinformatics (Winter term)
Syllabus
Lab manual
Download zone
Weekly schedule:
| Wk |
Chp |
Topic |
|
1 |
1 |
Lec: String-matching algorithms in BLAST and FASTA |
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Lab: Sequence database and heuristic string matching: NCBI Entrez, BLAST and DAMBE |
|
2 |
5, a, d |
Lec: Motif-characterizing algorithms |
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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 |
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Lab: RNA-Seq software demonstration only (~1 hr) |
|
5 |
8-9, b, f, j-l |
Lec: Amino acid and codon usage bias and indices |
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Lab: Codon Usage Bias |
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6 |
c, i, m |
Lec: Bioinformatics and translation initiation in prokaryotes and eukaryotes |
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1st mid-term exam+Lab: Secondary Structure, MFE And IRES |
|
7 |
10, n |
Lec: Evolution of acid-resistance in Helicobacter pylori |
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Lab: Genomic Isoelectric Point Profiling |
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8 |
2 |
Lec: Molecular phylogeneitcs+Sequence alignment by dynammic programming |
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Lab: Sequence Alignment |
|
9 |
13 |
Lec: Transition bias and substitution models |
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Lab: Choosing The Best-Fit Substitution Model |
|
10 |
13 |
Lec: Distance-based methods |
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Lab: Molecular Phylogenetics |
|
11 |
13, h |
Lec: Molecular clock |
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2nd mid-term exam+Lab: Testing The Molecular Clock Hypotheses |
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12 |
13, e |
Lec: Dating speciation and gene duplication events |
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Lab: Dating with the Least-Squares Method |
Additional reading materials:
- 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.
- 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
- 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
- Ma, P.,Ma, P., Xia X. 2011. Factors affecting splicing strength of yeast genes. Comparative and Functional Genomics. Article ID 212146, 13 pages
- Xia, X. , Yang, Q. 2011. A Distance-based Least-square Method for Dating Speciation Events. Molecular Phylogenetics and Evolution 59:342-353.
- 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
- Palidwor GA, Perkins TJ, Xia X. 2010. A General Model of Codon Bias Due to GC Mutational Bias. PLoS ONE 5(10): e13431.
- 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.
- Xia, X., Holcik, M., 2009. Strong Eukaryotic IRESs Have Weak Secondary Structure. PLoS ONE 4, e4136.
- Xia, X. 2008. The cost of wobble translation in fungal mitochondrial genomes: integration of two traditional hypotheses. BMC Evolutionary Biology 8:211.
- 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 .
- Xia, X. 2007. An Improved Implementation of Codon Adaptation Index. Evolutionary Bioinformatics 3:53–58.
- Xia, X. 2007. The +4G site in Kozak consensus is not related to the efficiency of translation initiation. PLoS ONE 2(2):e188.
- Xia, X. and G. Palidwor. 2005. Genomic Adaptation to Acidic Environment: Evidence from Helicobacter pylori. American Naturalist 166:776-784
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