Reconstruction Targets

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Broad classification of targets for ancestral sequence reconstruction

See also papers on Journal Club page.

Ancient genes

Human-clade gene sets


General large gene/domain sets

e.g. for answering general questions about protein evolution, or providing a resource for others

Questions that can be asked

* indel rate-2ndary structure relationship * indel size distribution * frequency (and source?) of 'large' loop insertions * grow-shrink behaviour in loops: are indels often nested? * can we propose mechanisms (or bounds on the number of mechanisms) by which indels occur (i.e. single-position, large inserts/recombination, etc...) * Harper & Keeling: Lateral gene transfer and the complex distribution of insertions in eukaryotic enolase. Gene 2004;340:227-35. * can we provide evidence for a 'continuum of stem topologies from short loops to mature protein domains' ?

* transposons can move transcription factors around at least in mammals. Does this happen in other species??

Genes of technological interest

Pharmaceutical targets

  • DHPS (Peat et al)

Biotechnology (enzymes, bioremediation etc)


-- Ian Holmes - 18 Oct 2008