RepeatMasker output

sydghyyh14 · 09-20-2011, 10:30 AM

I am interested in screening human genome sequences with RepeatMasker.

But I got some results like this in the .out file:

532 22.4 8.4 5.4 chr22 24022607 24022809 (27281757) + LTR87
LTR/ERVL? 414 622 (2) 11670
241 34.0 11.8 3.2 chr22 25658607 25658886 (25645680) +
LTR88c LTR/Gypsy? 7 310 (552) 14807
284 23.4 9.3 13.0 chr22 25916174 25916335 (25388231) +
LTR88b LTR/Gypsy? 666 821 (16) 15305
496 21.4 1.1 0.0 chr22 26283796 26283884 (25020682) +
UCON21 DNA? 89 178 (152) 15973
302 33.5 3.0 3.0 chr22 26455064 26455260 (24849306) + LTR89
LTR/ERVL? 683 879 (0) 16334
507 23.2 1.6 0.0 chr22 26550000 26550124 (24754442) +
MER124 DNA? 58 184 (213) 16545

I don't know why some class or family names followed by "?" character
(e.g. "LTR/Gypsy?").

nservant · 06-06-2012, 07:17 AM

Hi,

I also have the same question, about repeats family name and "?".
Did you have any answer ?
Thank you

Artem · 06-06-2012, 01:14 PM

I know that Gypsy LTR is usually found in Drosophila and I briefly read over one paper which said that they found Gypsy-like elements in humans, entering the genome 70mya and highly diverged. For an LTR/ERV this is quite old, most are in the range of 25-50 mya.

A definate answer as to what the ? means would be helpful to me as well.

rhubley · 09-11-2012, 04:26 PM

The "?" Following either a the family or the subfamily designations is an indication by the sequence curator that the assignment may be questionable. Over time as the repeat library improves these are removed and replaced with corrected or confidently stated designations.

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09-20-2011, 10:30 AM	#1
sydghyyh14 Junior Member Location: Beijng, China Join Date: Mar 2010 Posts: 7	RepeatMasker output I am interested in screening human genome sequences with RepeatMasker. But I got some results like this in the .out file: 532 22.4 8.4 5.4 chr22 24022607 24022809 (27281757) + LTR87 LTR/ERVL? 414 622 (2) 11670 241 34.0 11.8 3.2 chr22 25658607 25658886 (25645680) + LTR88c LTR/Gypsy? 7 310 (552) 14807 284 23.4 9.3 13.0 chr22 25916174 25916335 (25388231) + LTR88b LTR/Gypsy? 666 821 (16) 15305 496 21.4 1.1 0.0 chr22 26283796 26283884 (25020682) + UCON21 DNA? 89 178 (152) 15973 302 33.5 3.0 3.0 chr22 26455064 26455260 (24849306) + LTR89 LTR/ERVL? 683 879 (0) 16334 507 23.2 1.6 0.0 chr22 26550000 26550124 (24754442) + MER124 DNA? 58 184 (213) 16545 I don't know why some class or family names followed by "?" character (e.g. "LTR/Gypsy?").

06-06-2012, 07:17 AM	#2
nservant Junior Member Location: france Join Date: Oct 2008 Posts: 3	Repeats family name Hi, I also have the same question, about repeats family name and "?". Did you have any answer ? Thank you

09-11-2012, 04:26 PM	#4
rhubley Member Location: Washington Join Date: Sep 2012 Posts: 10	Family/Subfamily Designations The "?" Following either a the family or the subfamily designations is an indication by the sequence curator that the assignment may be questionable. Over time as the repeat library improves these are removed and replaced with corrected or confidently stated designations.

06-06-2012, 01:14 PM	#3
Artem Junior Member Location: Vancouver, BC Join Date: May 2012 Posts: 6	I know that Gypsy LTR is usually found in Drosophila and I briefly read over one paper which said that they found Gypsy-like elements in humans, entering the genome 70mya and highly diverged. For an LTR/ERV this is quite old, most are in the range of 25-50 mya. A definate answer as to what the ? means would be helpful to me as well.