How to collect the phastCons and phyloP data from Ensembl
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2.7 years ago
wangdp123 ▴ 250

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

Ensembl phastCons phyloP • 1.5k views
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wangdp123 : Don't forget to follow up on your threads.

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

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No, we did not do multiple alignments for them.

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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.

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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?

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

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