Biometry and bioinformatics II, fall 2014

Prerequisites: At least intermediate level of probability and statistical inference courses and basic familiarity to working with sequence data (such as provided by the course Biometry and bioinformatics I, for example). The spirit of the course is learning by doing assignments.

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=== (% style="color: rgb(0,51,102);" %)Short description of contents

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The ultimate goal is to provide understanding of life through molecular information, via statistical and computational analyses. Models of molecular evolution and phylogeny inference, going further from the basics which were in the course Biometry and bioinformatics I: maximum likelihood, bayesian and network inference. Past, or traditional, practice on phylogenetics has been to describe relationships among species within the disciplines systematics and taxonomy. Today the scope is much wider. Phylogenetics is used as a necessary tool in all kind of bioscience research questions: relationships among genes, gene families, alleles, cell lines, various genomic components, histories of populations, evolutionary and epidemiological dynamics of bacteria and viruses, etc. Phylomics is the natural extension of genomics and metagenomics, phylotyping the current way of understanding ecosystems within and outside organisms (environments) and evolutionary thinking is a complementary framework to medical genetics. Statistical and computational approaches, based on predictions derived from population genetics theory, aim at dissecting neutral (stochastic) and selected (darwinian natural selection) components of genetic diversity.

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=== (% style="color: rgb(0,51,102);" %)Time schedule

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(% style="color: rgb(0,0,0);" %)The first session will be Tuesday 4.11, 14-17, computer class C128(% style="color: rgb(153, 51, 0); color: rgb(0, 0, 0)" %)** **(% style="color: rgb(153,51,0);" %)** **(%%)(not 28.10 as the exam of Biometry and bioinformatics I is still going on).

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The assignments for 5-10 cr part of the course will be launched during the sessions 4.11 and 11.11. Working after these two common sessions can accomplished according to personal, and negotiable, time schedules. There will be no exam. Grading is based on the quality of assignments and pass/fail is also possible.(% style="color: rgb(0,51,102);" %)

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=== (% style="color: rgb(0,51,102);" %)**Lecture material and scientific publications

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* (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)[[attach:Modelling molecular evolution.pdf]], Literature:

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* (% style="color: rgb(0,51,102);" %)[[attach:Phylogeny inference methods.pdf]], (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)Literature: (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(0, 51, 102)" %) (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 51, 102)" %)[[attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@Phylogenetics - Principles and practice.pdf]](% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %),(% class="confluence-link" %) (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 51, 102); color: rgb(0, 51, 102)" %)[[attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@Short tutorial article.pdf]](% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %), [[attach:Original NJ-algorithm paper.pdf]], (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)[[attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@Original MrBayes paper.pdf]],(% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %) (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)[[attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@Traditional and Bayesian phylogeny estimation.pdf]], (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 0, 0); color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)[[MCMCMC.pdf,>>attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@MCMCMC.pdf]] [[attach:Felsenstein_Confidence limits on phylogenies.pdf]]

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=== (% style="color: rgb(0,51,102);" %)**Assignments**(%%) ===

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(% style="color: rgb(0,0,0);" %)You can choose which assignments you perform. Assignments 1, 2, 3 and 4 are 1 cr, each, assignment 5 will be 1-3 cr (depending on the amount of work you want to do). In addition, there will be essay topics (1 cr = 5 page essay about a topic, Assignments 6). You can also tailor a molecular evolutionary project for yourself about an interesting gene, or some other genomic compartment.

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* (% style="color: rgb(0,51,102);" %)[[attach:Assignment_1 BB_II.pdf]]

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* (% style="color: rgb(0,51,102);" %)[[attach:Assignment_2 BB_II.pdf]]

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* (% style="color: rgb(0,51,102);" %)[[attach:Assignment_3 BB_II.pdf]]

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* (% style="color: rgb(0,51,102);" %)[[attach:Assignment_4 BB_II.pdf]]

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* (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)Assignment 5(% style="color: rgb(0,51,102);" %) (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)will be(% style="color: rgb(0,51,102);" %) (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)about EBOLA. Read these: (%%)[[EBOLA phylogenetics.pdf>>url:http://wiki.helsinki.fi/download/attachments/135070013/EBOLA%20phylogenetics.pdf?version=1&modificationDate=1412074592234&api=v2||shape="rect"]] , [[attach:EBOLA_Phylogenetics_2.pdf]], and start getting familiar with the existing data in NCBI nucleotide database![[attach:Recent news_ Delays hinder EBOLA genomics.pdf]]

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* (% style="color: rgb(255,0,0);" %)**Assignment 6, topics:**(%%)

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[[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_history_1.pdf]], [[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_history_2.pdf]]

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[[attach:Protein_evolution_1.pdf]], [[attach:Protein_evolution_2.pdf]], [[attach:Protein_evolution_3.pdf]], [[attach:Protein_evolution_4.pdf]], [[attach:Protein_evolution_5.pdf]]

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[[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_cancer_1.pdf]], [[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_cancer_2.pdf]], [[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_cancer_3.pdf]], [[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_cancer_4.pdf]], [[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_celltypes.pdf]], [[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_languages.pdf]]

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[[attach:Phylo_virus_1.pdf]], [[attach:Phylo_virus_2.pdf]], [[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_bacteria_1.pdf]], [[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_bacteria_2.pdf]], [[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_lateral gene transfer_1.pdf]], [[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_lateral_gene_transfer_2.pdf]]

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[[attach:Phylo_mammals_1.pdf]], [[attach:Phylo_mammals_2.pdf]]

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[[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_metagenomics_methods.pdf]], [[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_human_metagenomics_1.pdf]], [[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_human_metagenomics_2.pdf]], [[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_env_metagenomics_1.pdf]], [[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_env_metagenomics_2.pdf]]

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[[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_statistics_1.pdf]], [[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_statistics_2.pdf]], [[attach:mathstatKurssit.Phylogeny inference and data analysis, fall 2013.WebHome@Phylo_HMM_2.pdf]]

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=== (% style="color: rgb(0,51,102);" %)**Datafiles**(%%) ===

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* (% style="color: rgb(0, 51, 102); color: rgb(0, 51, 102)" %)[[attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@data_1.txt]]

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* (% style="color: rgb(0, 51, 102); color: rgb(0, 51, 102)" %) (% style="color: rgb(0,51,102);" %)[[attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@data_2.txt]]

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* (% style="color: rgb(0,51,102);" %)[[data_3.txt,>>attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@data_3.txt]] [[data_3_aligned.txt,>>attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@data_3_aligned.txt]] [[attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@data_3_aligned_IUPACedited.txt]]

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* (% style="color: rgb(0,51,102);" %)[[attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@data_4.fasta]]

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* [[attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@data_HLA_gene.fasta]]

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=== (% style="color: rgb(0,51,102);" %)**Software**, **servers, links to databases**(%%) ===

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* [[http:~~/~~/www.ncbi.nlm.nih.gov/,>>url:http://www.ncbi.nlm.nih.gov/||shape="rect"]] Literature: [[attach:mathstatKurssit.Biometry and bioinformatics I, fall 2013.WebHome@NCBI BLAST.pdf]],

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* ClustalX2 (in C128), [[http:~~/~~/www.ebi.ac.uk/Tools/msa/clustalw2/,>>url:http://www.ebi.ac.uk/Tools/msa/clustalw2/,||shape="rect"]] [[(% style="color: rgb(0,0,0);" %)Literature:(%%) Multiple sequence alignment.pdf>>attach:mathstatKurssit.Biometry and bioinformatics I, fall 2013.WebHome@Multiple sequence alignment.pdf]],

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* [[http:~~/~~/mafft.cbrc.jp/alignment/server/>>url:http://mafft.cbrc.jp/alignment/server/||shape="rect"]]

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* [[MEGA5>>url:http://www.megasoftware.net/||shape="rect"]] (% style="color: rgb(0,0,0);" %)(in C128), Literature: (% class="confluence-link" %)[[MEGA5 original paper.pdf,>>attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@MEGA5 original paper.pdf]] (% style="color: rgb(0,51,102);" %)

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* (% class="confluence-link" %) (%%)[[DnaSP5-software>>url:http://www.ub.edu/dnasp/||shape="rect"]] (% style="color: rgb(0,0,0);" %)(in C128),

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* (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)[[MrBayes-software>>url:http://mrbayes.sourceforge.net/||shape="rect"]] (in C128), Move the file (the training file primates.nex) to Z, and when strating MrBayes: execute z:\primates.nex, [[MrBayes Manual 3.1.pdf,>>attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@MrBayes Manual 3.1.pdf]] (% style="color: rgb(0,51,102);" class="confluence-link" %) (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)[[attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@MrBayes Commands.pdf]], [[attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@This is useful clarification.pdf]],

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* (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)[[Link to data-conversion>>url:http://sequenceconversion.bugaco.com/converter/biology/sequences/||shape="rect"]] (use this, or use Clustal, for obtaining a nexus-format from the data so that it can be submitted to MrBayes)

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* (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 0)" %)[[Link to choosing a model>>url:http://www.hiv.lanl.gov/content/sequence/findmodel/findmodel.html||shape="rect"]] (note also model choice option in MEGA5) [[attach:mathstatKurssit.Biometry and bioinformatics II, fall 2013.WebHome@Modeltest.pdf]](%%) ,[[attach:This is useful, AIC.pdf]]\\

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* [[SIFT>>url:http://sift.jcvi.org/||rel="nofollow" shape="rect" class="external-link"]] (Sorting Intolerable From Tolerable) and [[PolyPhen>>url:http://genetics.bwh.harvard.edu/pph2/||rel="nofollow" shape="rect" class="external-link"]] (prediction of functional effects of human nsSNPs)

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=== **[[BB_II_MOODLE>>url:https://moodle.helsinki.fi/course/view.php?id=14735||shape="rect"]]** ===

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=== (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 128); color: rgb(0, 51, 102)" %)**Background literature, e-books in HU-library**

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* (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 128); color: rgb(0, 51, 102)" %)[[Z Yang, Computational molecular evolution>>url:http://ukcatalogue.oup.com/product/9780198567028.do||shape="rect"]]

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* (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 128); color: rgb(0, 51, 102)" %)[[P Lemey et al, The phylogenetic handbook>>url:http://www.cambridge.org/us/academic/subjects/life-sciences/genomics-bioinformatics-and-systems-biology/phylogenetic-handbook-practical-approach-phylogenetic-analysis-and-hypothesis-testing-2nd-edition||shape="rect"]]

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* (% style="color: rgb(0, 51, 102); color: rgb(0, 0, 128); color: rgb(0, 51, 102)" %)[[M Nei and S Kumar, Molecular evolution and phylogenetics>>url:http://mep.asu.edu/||shape="rect"]]

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