Question

Conservation of Human and Mouse DNA sequences

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4.9 years ago

fusion.slope ▴ 250

Hello,

i have a list of DNA regions from mouse ESCs and I would like to know if these sequences are conserved also in Human. How can I do this?

Comparative Genomic Conserved DNA regions • 993 views

ADD COMMENT • link updated 4.9 years ago by JC 13k • written 4.9 years ago by fusion.slope ▴ 250

score 2 · Answer 1 · 2020-01-13

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4.9 years ago

JC 13k

you can use UCSC GB LiftOver tool

ADD COMMENT • link 4.9 years ago by JC 13k

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do you think it is enough?

ADD REPLY • link 4.9 years ago by fusion.slope ▴ 250

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do you think it is enough?

That you will need to decide.

If the right regions are present in the dataset you could also look at precomputed information available here from JAX.

ADD REPLY • link 4.9 years ago by GenoMax 147k

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What i am doing i am lifting the coordinates of mouse to human as also the coordinates of human to mouse. Then on the lifted coordinates i calculate the conservation score using phasCons in UCSC table browser. I simulate also a set of sequences with similar GC content, size and nucleotide composition of the lifted sequences and I compute again the conservation score. Then i compare the conservation scores of these files..

Does this make sense?

ADD REPLY • link 4.9 years ago by fusion.slope ▴ 250

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Not sure why you are doing this so can't say.

ADD REPLY • link 4.9 years ago by GenoMax 147k