phylop

[Neeba Dijo]

Hello,

I am using  phlylop conservation scores and it conatins positive and negative values.

Is there is any range for phylop score

I think phastcon have a range of 0- 1

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Thanks & Regards,

Neeba Sebastian

[Brian Lee]

Dear Neeba Sebastian,

Thank you for using the UCSC Genome Browser and your question about if there is any range for phyloP scores.

You are correct that phastCons scores range from 0 to 1, while phyloP conservation scores contain positive and negative values.

You can read more about each method in the Conservation Track's Description page: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way

For example, here is a helpful paragraph from the page describing phyloP and phastCons: "Another important difference is that phyloP can measure acceleration (faster evolution than expected under neutral drift) as well as conservation (slower than expected evolution). In the phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue), while sites predicted to be fast-evolving are assigned negative scores (and shown in red). The absolute values of the scores represent -log p-values under a null hypothesis of neutral evolution. The phastCons scores, by contrast, represent probabilities of negative selection and range between 0 and 1."

To obtain a range for phyloP scores, you can use the Table Browser and use the "summary/statistics" button on the desired phyloP* table.

1. Navigate to the Table Browser: http://genome.ucsc.edu/cgi-bin/hgTables?command=start

2. Make the following selections, picking a desired phyloP* table:

Clade: Mammal

Genome: Human

Assembly: Feb. 2009 (GRCh37/hg19)

Group: Comparative Genomics

Track: Conservation 

Table: phyloP* (For example phyloP46wayAll)

3. Make sure you have "region: genome" selected.

4. Click the "summary/statistics" button/

You will then get summary output for each showing the range of scores from Minimum, Maximum and Range. For example the values for the table phyloP46wayAll on chr1 are: -11.764; 6.424; 18.188. For comparison, another example of values for the values for the table phyloP46wayPrimates on chr1 are: -0.378858; 0.447276; 0.826134.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have further questions, please feel free to contact the mailing list again at gen...@soe.ucsc.edu.

All the best,

Brian Lee

UCSC Genome Bioinformatics Group

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