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Get Conservation Score Of Chromosome Region

Dear All,

I want to ask if there is a good tool or website can figure out the conservation score (like phastcons) for a chromosome region, eg. chr1:1617197-1617281(human).

Phastcons give the score for each site but not for a region. I am not sure if that is correct to get the mean score of phastcons score at all sites in that region.

Can anyone help this.

Thanks very much.

Che

conservation
• 7,210 views • link
updated by Ian Ian • written by camelbbs camelbbs

2 answers

Use UCSC table browser wisely and you will get them.

  1. Select GROUP - Comparative Genomics
  2. Select TRACK - Conservation
  3. Select TABLE - PhastCons
  4. Check Position
  5. Paste your genomic co-ordinates using "defined regions" button
  6. Go!
• 105 views • link
written by biorepine biorepine

Note that phastCons and phyloP scores are not available at unmappable bases, so it may make sense to filter regions before applying them.

• 0 views • link
written by Alex Reynolds Alex Reynolds

Thanks very much. But I think that will give scores for each nt, Can I average the scores for a range?

• 0 views • link
written by camelbbs camelbbs

Table browser can not do that in my knowledge. However, you can download phastcons scores from UCSC and write a small script to calculate averages.

• 0 views • link
written by biorepine biorepine

For the sake of completeness i once gave this answer to a similar question:

Measuring Conservation For Short Motif

Quite long winded though :)

• 184 views • link
written by Ian Ian

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