Request for multiple alignment file and phastCons scores with new tree shrew and rabbit genome

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Lin Ou

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Oct 10, 2025, 3:32:58 PM (4 days ago) Oct 10

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Dear UCSC staff:

I'm a Ph.D candidate from Tsinghua University. Recently I want to explore the conservation score (phastcons scores) in some regulatory elements of tree shrew and rabbit.

However, so far there lacks available phastcons scores with tree shrew or rabbit genome as reference genome from the website. Besides, even though I found the valuable resource 447-way mammalian alignment (so amazing!), it doesn’t include the specific species with specific genome version (which we used for sequence data analysis):

The rabbit genome (OryCun3.0):

https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_013371645.1/

The tree shrew genome (Genome assembly KIZ version 2):

https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_033439345.1/

Could you give me some advice on this condition (any advice would be helpful)? Or, I wonder could you help us to make a new multiple alignments and calculate phastcons scores(even helpful) using these new genome versions? I know it is a resource-costing and time-consuming process, could you please make a small-scale alignment first if possible (e.g human(hg38), mouse(mm10), pig(susScr11), rabbit(GCA_013371645.1), tree shrew(GCA_033439345.1), Mouse lemur(micMur2))? Or include some more mammals or vertebrates?

By the way, I don’t understand well whether there is big difference on phastcons scores when calculating with different-scale alignment files. I will appreciate it if you could explain it further to me.