Get Conservation Score Of Chromosome Region

Question

[camelbbs]

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

Answer 1

[biorepine]

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!

[Alex Reynolds]

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

[camelbbs]

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

[biorepine]

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.

Answer 2

[Ian]

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

Measuring Conservation For Short Motif

Quite long winded though :)