ESIL :: 1ère année :: Module "Bioinformatique" :: année 2011/2012 :: Raphaël Bourgeas & Jacques van Helden

Session 1: [TITLE]


Contents


Introduction


Resources

Name Link Description
Phylogeny.fr Phylogenic inference Robust Phylogenetic Analysis For The Non-Specialist.
http://phylogeny.lirmm.fr/
http://www.phylogeny.fr/
Taxonomy browser Taxonomy http://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cgi

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Inferring the phylogeny of opsins in Mammals

Context

Goals of this exercise

Tips

  1. The absence of a protein in a database may result from many reasons (genome not completely sequenced, sequencing holes, incompleteness/errors in the annotations). It is thus generally not sufficient to indicate its absence in the considered organism.
  2. After you ran a query in Uniprot, the head of the result page displays an option that allows you to restrict the resutls to completely sequenced genomes.

Questions

  1. In Uniprot, find all the opsins for the Mammals whose genome has been completely sequenced.
  2. Select a subset of 5 species, and extract their sequences in fasta format.
  3. Submit the sequences to the Phylogeny.fr Web server. How do you interpret the result ? Can you infer an evolutionary scenario from the resulting tree ? How does it compare with the conclusions drawn from the practical on pairwise sequence comparisons ?

Raphaël Bourgeas (IMR, Université de Provence) & Jacques van Helden (TAGC, Université de la Méditerranée).