Reverse Transcriptase Copy Number

Question

[Alastair Kerr]

Anyone know of a data source that would provide information on how many copies there are of reverse transcriptase in the human genome. (i.e. from Lines/Sines etc ).

Ideally 2 numbers, the number complete and the number truncated.

I feel that this info should be available some-place but I have not found been able to find it.

Any ideas? Or is it BLAST time?

[Vikas Bansal]

Do you mean the number of SINE, Lines etc in genome?

[Alastair Kerr]

Almost, the problem is that not all contain an intact reverse transcriptase. Thanks for your answer though as it is a reasonable approximation

Answer 1

[Vikas Bansal]

I am not sure if this is what you want. If you want information about Lines, Sines etc, I think RepeatMasker is the good option and for humans (also for some other species) the data is already present in UCSC. Also a very good review by Todd and Steven on Repetitive DNA and next-generation sequencing: computational challenges and solutions is given here. I pasted a table from their paper which is taken from RepeatMasker annotation itself.