RepeatMasker question

[Askree, Hussain]

Hello,

 

I have been trying to figure out what exactly is calculated as the “divergence” for repeats annotated under this track. I can not find the answer in Repbase updates. Would someone in your team be able to guide me about this?

 

Thank you for your time.

 

Most sincerely,

 

Hussain

 

 

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[Jonathan Casper]

Hello Hussain,

Thank you for your question about the divergence values displayed for items in the RepeatMasker track. These values are calculated by the RepeatMasker software, and your best source of information on this topic is most likely to contact the authors directly. That said, the information in http://www.repeatmasker.org/webrepeatmaskerhelp.html suggests that the divergence value is simply the percentage of bases in the matching region that were substitutions with respect to the consensus repeat sequence.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

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[Askree, Hussain]

Jonathan,

 

Thank you a million. I do not know how I managed to miss the help page.

 

I am a huge fan of the browser. Thank you!

 

h