obtain AT-rich coordinates hg19

Question

[2nelly]

Hi all,

Does anybody know a source to download AT rich regions for hg19?

thank you in advance

[finswimmer]

Hello 2nelly,

could you please explain what AT content is AT rich for you? How many bases should the region be long at least?

fin swimmer

[2nelly]

I don t know exactly ,but something analogous to CG rich content.

i am wondering if there is a source like the UCSC that i can find this information.

[finswimmer]

I don t know exactly

That's not good ... Let's try it the other way round to find a better definition. Why do you need those regions?

fin swimmer

[2nelly]

ARS in yeast is related to AT rich areas.

Thence, I am wondering if there is any correlation of AT rich areas with human Origins of replication.

This is not clear yet.

Answer 1

[Manu Prestat]

You may find what you are looking for with adding the keyword "isochores". For example:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4662427/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1457033/

Bu this is a "macro" definition ("[...] long (>200 kb) DNA sequences that are fairly homogeneous in base composition[...]"). You could look at this metric at higher resolution.

[2nelly]

Sounds promising! But i believe that it requires more effort on this direction to clearly identify those regions. Thanks!