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mariodosreis / tai

The tRNA adaptation index
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Mouse tRNA #5

Closed kir1to455 closed 2 weeks ago

kir1to455 commented 2 weeks ago

Hi Mario,

First of all, thank you for developing this tool.

The first question is how to define the s-values of different species? Like Homo or Mouse? image

The second question is how to define the tRNA pool between different tissues of the same species to calculate tAI? If I have DM-tRNA-seq of brain and heart tissues, and the content of anti codon tRNA in each tissue is different, how should I calculate the tAI value?

Best wishes, Kirito

mariodosreis commented 2 weeks ago

Hi closing this issue as this is not a software issue but rather a research one.

I note s-values for other species could be estimated as done originally for yeast, i.e., by obtaining expression data and optimising the correlation between expression and tAI. This has been done by other groups and there are papers and databases available from Tuller's group about this (sorry can't remember the references out of my head). Tissue specific s-values could be calculated in a similar manner.