Download Practical 1 - Institut Pasteur

Practical 1
Predicting orthology for two
homologous gene families
Species tree
Gene tree
Gene tree
Gene tree
(((((5_human:0.04, 6_human:0.04):0.03,
(7_human:0.06,
8_human:0.06):0.01):0.06,
((1_mouse:0.30, 2_mouse:0.30):0.09,
(3_mouse:0.18,
4_mouse:0.18):0.21):0.02):0.03,
9_dog:0.18):0.5,
((10_human:0.13, 11_mouse:0.40) :
0.03, 12_dog:0.18):0.5);
Prot dist trees can be misleading
Prot dist trees can be misleading
Practical
• Sequences created with evolver
• N.B. evolver takes tau(t)
t = 3 dS * S / (S + N) + 3 dN * N / (S + N)
• Try calculating trees with protdist and codeml
dS and TreeBesT.
• Are they the same? Why not?
Practical 2
Functional inference for a mouse
highly duplicated gene families
Functional annotation
• How many are there?
• Where are they found?
• Are the genes protein coding?
http://www.ch.embnet.org/software/ClustalW.html
http://coot.embl.de/pal2nal/#RunP2N
• Do they contain functional domains?
http://smart.embl-heidelberg.de/
http://www.ebi.ac.uk/interpro/
• Can we infer function?
http://www.ncbi.nlm.nih.gov/pubmed/!!
• Can you sum this up in less than three sentences
My summary
XLR superfamily includes members whose imprinted
expression in the brain are associated with X-linked
parent-of-origin effects on cognitive function. Most
members of this family show testes expression
including the meiosis regulated Xmr/Slx which are
present in greater than 70 copies, depending on the
mouse strain, in the mouse X and Y chromosomes.
Xmr/Slx paralogs may play a part in post-meiotic Xversus-Y chromosome intragenomic conflict in
spermatid cytoplasm.