How to collect the phastCons and phyloP data from Ensembl

Question

[wangdp123]

Hi there,

Does anybody know if Ensembl/Ensemblgenomes provides the data of sequence conservation scores (e.g., phastCons, phyloP) for each nucleotide of the genomes? If so, where to download the data?

Many thanks,

Tom

[GenoMax]

wangdp123 : Don't forget to follow up on your threads.

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

Please do the same for your previous posts as well.

Answer 1

[Emily]

GERP conservation scores here.

[wangdp123]

Thanks Emily. Are there any conservation scores for Ensemblgenomes database (http://ensemblgenomes.org/) such as Ensembl Fungi, Ensembl Plants, Ensembl Protists and Ensembl Metazoa?

[Emily]

No, we did not do multiple alignments for them.

Answer 2

[Santosh Anand]

You may easily get them from UCSC (Google it). The reference genome assembly doesn't change between different sites - so it will give the same info.

[Kevin Blighe]

Indeed, link for hg38: http://hgdownload.cse.ucsc.edu/goldenpath/hg38/

[wangdp123]

Thanks. Any idea about how to get the conservation scores for each gene or exon by making use of the single nucleotide data? I know that the bigwig files contain the conservation score for each nucleotide. Should we use the sum or mean to calculate the scores for single gene or exon?

[Kevin Blighe]

That is a design choice that you should make. For me, calculating mean per sliding window interval makes sense.