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Biometry and bioinformatics I, fall 2014


Lecturer

Sirkka-Liisa Varvio

Scope, type and prerequisites

  • 5 cr (-> 10 cr by additional work)
  • Intermediate / advanced studies in statistics
  • At least basic courses on probability and statistical inference are assumed as prerequisites

Time schedule and content scheme and relationships to other courses

  • Tuesdays 14-18 in computer class C128, Exactum
  • I period. The first session will be 9.9
  • The course consists of tutorial lectures during computer sessions, assignments initiated during computer session (completed during student´s own, additional, time).
  • The spirit of the course is  learning by doing (data-analysis) and reading scientific papers, rather than listening lectures. The general topic is: how to work with sequence data, collecting data from databases - the first steps which are need in the next course, Biometry and bioinformatics II. BB_II.
  • Assignments 1, 2 and 3 to be submitted 7.10 at the latest. They will be inspected and commented. Assignments 4 and 5 to be submitted 13.10.
  •  Home-exam.

Computer session 9.9.14 in C128,  14.15 ->

We familiarize with http://www.ncbi.nlm.nih.gov/, NCBI BLAST.pdf. Examples.

Introduction to sequence alignment by ClustalX, http://www.clustal.org/, (installed in C128, ); also http://mafft.cbrc.jp/alignment/server/ will be introduced

The plan is that after this session you are prepared to start data collection to assignments 1 and 2. Next session, 16.9 is a tutorial session for data collection for these two assignments.
Submit your collected data for assignment 1 to course Moodle-area. It will be checked and commented by Mitja or Siru. No data pre-checking for assignment 2.
During the session 23.9 there is a lecture about sequence clustering methods.

Computer session 16.9 in C128, 14.15 ->

Data-collection for assignments 1, 2 and 3.                                                                                               

Assignment 3_ BB_I.pdf, Human mitochondrial genome database: http://www.mtdb.igp.uu.se/

Lecture session 23.9 in C128, 14.15 ->

Data-analysis session 30.9 in C128, 14.15 ->

  • The session is for practical data-analysis with MEGA5. You should have your data for assignments 1, 2 and 3 collected, and ready to perform phylogeny analyses. Next Tuesday, 6.10 you are supposed to submit your reports.
     

Session 14.10 in C128,    

  • Assignment 1,2 and 3 presentations

 

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