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How to download article publication data from UCSC genome browser

Recently I read a paper named " Identification of constrained sequence elements across 239 primate genomes", which provide 239 primate species whole-genome multiple sequence alignment file.

I want to download this MSA file. In data availability section, it's said "The MSA and constraint tracks are available through the UCSC Genome Browser", but I failed to find the way to download this file from UCSC genome browser. I have only downloaded sone genome data from this website before, and I'm not sure how to download article publication data from it.

I have emailed the author of the article to inquire, but have not received a reply yet

Thanks a lot for any advice!

msa ucsc
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written by Yurun • Yurun

Thanks a lot for replying ! I know this data, and it's from another paper published by zoonomia project.

It seems that my data source article integrated 239 primates with this data, finally producing the 447-way alignment result. Maybe they only release the integrated file. I'll try to remove non-primate genome from 447-way alignment to get pure primate MAF file.

Thank you once again for your response ^_^

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written by Yurun • Yurun

1 answer

You can find this alignment in the 'Cactus 447way' track: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=cons447way

Maf file download available: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus447way/

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updated by Ram Ram • written by nullmodel • nullmodel

Just a note, 447-way alignment includes organisms besides the primates. OP was asking about primates specifically.

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written by GenoMax GenoMax

The Cactus 447-way alignment contains the referenced 239 primate genomes. There is no specific track by itself that has the 239 primate genomes. The zoonomia 241-way alignment is a much older project that also happens to be included in this 447-way alignment.

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written by nullmodel • nullmodel

The zoonomia 241-way alignment is a much older project

I will move my answer to a comment in light of that. OP seemed to indicate that the paper they read made it sound like this information was available via UCSC. Perhaps it was an older paper they read for the data I had linked above.

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written by GenoMax GenoMax

Thank you very much for the link! This helps me a lot. Exactly as GenoMax said I wanted pure primates MAF file, but I believe I could do some processing on this file to get it. Really appreciate your assistance ^_^

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written by Yurun • Yurun

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