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Predicting Orthology and Functional Inference for Homologous Gene Families in Mouse

This practical guide focuses on predicting orthology for two homologous gene families and explores functional inference for highly duplicated mouse genes. It emphasizes the potential pitfalls of protein distance trees and provides methods for calculating gene trees using ProtDist and CODEML. Furthermore, it investigates gene distribution, coding potential, and functional domains in gene families, particularly those related to cognitive function in X-linked superfamilies. Resources and tools are provided to enhance analysis accuracy and understanding.

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Predicting Orthology and Functional Inference for Homologous Gene Families in Mouse

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  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.

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