PhastCon scores?

[Jackie Jia Zhou]

Hi,

I downloaded the phastCon scores for rat with other 8 vertebrates from this link : http://hgdownload.soe.ucsc.edu/goldenPath/rn4/phastCons9way/

I have a couple of questions regarding the files/scores:

1) There are many genomic regions (the genomic coordiates in these regions are not in the downloaded files) that do not have a phastCon score in the file, why is that? does that mean these regions are not conserved at all? can I treat these regions as having a score=0 when handling the file?

2) Is there any threshold value for conservation score based on which we can define a particular block of gene to be ideally conserved?

Thank you,

-Jackie

[Steve Heitner]

Hello, Jackie.

Often, the description page will answer many of these types of questions.  In the case of your first question, the Methods section of the Conservation track description page (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=rn4&g=multiz9way) states:

“PhastCons currently treats alignment gaps as missing data, which sometimes has the effect of producing undesirably high conservation scores in gappy regions of the alignment. We are looking at several possible ways of improving the handling of alignment gaps.”

For your second question concerning ideally conserved elements, you should see the Most Conserved track, also in the Comparative Genomics section.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.

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Steve Heitner
UCSC Genome Bioinformatics Group

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