Biometry and bioinformatics I, fall 2013

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= (% style="color: rgb(0,51,102);" %)Biometry and bioinformatics I, fall 2013(%%) =

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

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[[Sirkka-Liisa Varvio>>doc:mathstatHenkilokunta.Varvio, Sirkka-Liisa]](% style="color: rgb(0,51,102);" %)

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===== (% style="color: rgb(0,51,102);" %)Scope, type and goal(%%) =====

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(% style="color: rgb(0,0,0);" %)2-5 cr

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(% style="color: rgb(0,0,0);" %)Submitting assignments during the two course weeks = 2 cr. (%%)Pass/fail.

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(% style="color: rgb(0,0,0);" %)Extra assignments after the course = 1-3 additional credits.

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This short course gives very basic practicals for working with biological sequence data and databases: making sequence queries ("blasting"), introduction to different kind of sequence databases, aligning seqs and clustering them.

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(% style="color: rgb(0,0,0);" %)If you have taken the course //Genetic analysis and molecular evolution// previously (or know how to work with biological sequence databases from some other previous course), then //Biometry and bioinformatics I// is not for you and you can start from //Biometry and bioinformatics II//.

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However, if you already know how to work with sequence data /sequence databases (for example on the basis of //Genetic analysis and molecular evolution//), you can take this course (without a need to participate the computer sessions) as assignments will not be the same as previously.

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(% style="color: rgb(0,0,0);" %)The contents of this BBI has previously been the introductory part of the course Genetic analysis and molecular evolution(%%). (% style="color: rgb(0,0,0);" %)If you have taken this old course(%%) (or know the abovementioned basics from some other course),

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- you can do the assignments and get the credits (the assignments will not be identical with those you have already done in Genetic analysis and molecular evolution)

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- but (% style="color: rgb(0,0,0);" %)you need not come to attend the sessions, starting Tuesday, 10.9, 14.15 - 17.00 in C128. In fact: do not come because the course will be very big, 24 computers, 38 students.(%%)

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So, if this address [[http:~~/~~/www.ncbi.nlm.nih.gov/>>url:http://www.ncbi.nlm.nih.gov/||shape="rect"]] is familiar, don´t come, just wait for the assignments to appear in course webpage.

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(% style="color: rgb(0,0,0);" %)

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(% style="color: rgb(0, 0, 0); color: rgb(0, 51, 102)" %)**Computer session 10.9, C128, 14.15 - 17**

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|(% class="highlight-blue" data-highlight-colour="blue" %)(((

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[[http:~~/~~/www.ncbi.nlm.nih.gov/>>url:http://www.ncbi.nlm.nih.gov/||shape="rect"]],[[

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NCBI BLAST.pdf>>attach:NCBI BLAST.pdf]]

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[[attach:TUTORIAL - collecting data from NCBI.pdf]][[

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Initial_dataset_for_tutorial.txt

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Initial_dataset_for_tutorial_aligned.fasta>>attach:Initial_dataset_for_tutorial_aligned.fasta]]

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)))

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(% style="color: rgb(0,51,102);" %)**Computer session 12.9, C128, 14.15 - 18**

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|(% class="highlight-blue" data-highlight-colour="blue" %)(((

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We check your proceeding with the tutorial example.

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Introduction to sequence alignment by Clustal (installed in C128); also [[http:~~/~~/mafft.cbrc.jp/alignment/server/>>url:http://mafft.cbrc.jp/alignment/server/||shape="rect"]] will be introduced.[[

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Multiple sequence alignment.pdf>>attach:Multiple sequence alignment.pdf]]

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Introduction to clustering by [[http:~~/~~/www.megasoftware.net/>>url:http://www.megasoftware.net/||shape="rect"]] (installed in C128).

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[[attach:Assignment 1_ BBI.pdf]],[[attach:gene.txt]]

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(% style="color: rgb(0,51,102);" %)**Computer session 17.9, C128, 14.15 - 17**

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|(% class="highlight-blue" data-highlight-colour="blue" %)(((

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[[attach:Assignment 2_BBI.pdf]],(% style="color: rgb(255,0,0);" %) (%%)[[

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http:~~/~~/www.ncbi.nlm.nih.gov/genomes/FLU/aboutdatabase.html>>url:http://www.ncbi.nlm.nih.gov/genomes/FLU/aboutdatabase.html||shape="rect"]]

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)))

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(% style="color: rgb(0,51,102);" %)**Computer session 19.9, C128 14.15 - 18**

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|(% class="highlight-blue" data-highlight-colour="blue" %)(((

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Working with assignments 1 and 2.

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

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Extra assignments, submission deadline 31.12.2013**

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|(% class="highlight-blue" data-highlight-colour="blue" %)(((

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(% style="color: rgb(255, 0, 0); color: rgb(0, 0, 0)" %)[[attach:Assignment 3_ BBI.pdf]] [[Human mitochondrial DNA database>>url:http://www.mtdb.igp.uu.se/||shape="rect"]]

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(% style="color: rgb(255, 0, 0); color: rgb(0, 0, 0)" %)[[attach:Assignment 4_BBI.pdf]] [[Tree of life website>>url:http://tolweb.org/tree/||shape="rect"]] [[attach:gene_1.txt]] [[attach:gene_2.txt]] [[attach:gene_3.txt]] [[attach:mt_genomes.txt]][[attach:mt_genomes_aligned.txt]]

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(% style="color: rgb(255, 0, 0); color: rgb(0, 0, 0)" %)[[attach:Assignment 5_BBI.pdf]]

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|=(% class="highlight-blue" data-highlight-colour="blue" %)(((

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====== [[BB I - Moodle>>url:https://moodle.helsinki.fi/course/view.php?id=10431||shape="rect"]] ======

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