1 / 11

Practical 1

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,

tambre
Download Presentation

Practical 1

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Practical 1 Predicting orthology for two homologous gene families

  2. Species tree

  3. Gene tree

  4. Gene tree

  5. 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);

  6. Prot dist trees can be misleading

  7. Prot dist trees can be misleading

  8. 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?

  9. Practical 2 Functional inference for a mouse highly duplicated gene families

  10. Functional annotation • How many are there? • Where are they found? • Are the genes protein coding?http://www.ch.embnet.org/software/ClustalW.htmlhttp://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

  11. 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 X-versus-Y chromosome intragenomic conflict in spermatid cytoplasm.

More Related