[Yossef Alexander Finkelberg]

Dear Sir or Madam,

I was wondering where can I get a list of prototypical sequences of repetitive elements that were used to create the RepeatMasker table? The Repbase Update database contains sequences for some, but not all sequences from the table (at least when I am trying to directly compare RE ids).

Thank you very much!

Kind regards,

Joseph Finkelberg

J

[Matthew Speir]

Hello, Joseph.

Thank you for your question about RepeatMasker data in the UCSC Genome Browser.

Here is what one of our engineers noted regarding the way Repeatmasker builds matches:

When analyzing the data tables of this track, keep in mind that Repbase is not the same as the RepeatMasker sequence database and that the repeat names in the RepeatMasker output are not the same as the sequence names in the RepeatMasker database. This is because RepeatMasker creates annotations by joining matches to partial pieces of the database together so there is no 1:1 relationship between its sequence database and the annotations.

For example, the item "L1PA4" in the RepeatMasker output and this track might be constructed using the elements "L1PA_3p" and "L1PA5_5p" from the RepeatMasker database, but there is not necessarily a single sequence "L1PA4" in the RepeatMasker database.

We've also added similar text to the description page for the RepeatMasker track.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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Matthew Speir

UCSC Genome Browser, User Support

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