help in Repeat Masker

rahbz · 06-04-2013, 01:23 AM

Can any of you please let me know the interpretation of the repeat families

This is the part of .out file generated by the RepeatMasker

736 26.0 0.6 1.1 chr19 8015 8193 (299) C Eulor5B DNA? (0) 192 15 48785
390 26.9 4.3 10.0 chr19 76047 76220 (93229) C MamRep4096 DNA/hAT? (154) 272 107 48278
390 26.9 4.3 10.0 chr19 76851 76886 (92563) C MamRep4096 DNA/hAT? (320) 106 73 48278
523 25.6 15.0 0.0 chr19 3304 3463 (1384) C MER91A DNA/hAT-Tip100 (11) 185 2 40
268 25.2 4.8 16.2 chr19 6863 6996 (167262) + Charlie7a DNA/hAT-Charlie 1 122 (150) 99
268 25.2 4.8 16.2 chr19 7129 7217 (167041) + Charlie7a DNA/hAT-Charlie 123 203 (69) 99
268 25.2 4.8 16.2 chr19 7459 7527 (166731) + Charlie7a DNA/hAT-Charlie 204 265 (7) 99

What does DNA and DNA? mean
What does a question mark indicate at the end of the family.
Thank you in advance,

rhubley · 06-11-2013, 11:06 AM

The "DNA" class stands for DNA Tranposon -- a cut and paste type of interspersed repeats.

rahbz · 06-11-2013, 11:22 PM

Yah but what does 'DNA?' mean
what is the difference between 'DNA' and 'DNA?'

rhubley · 06-12-2013, 09:39 AM

Sorry, I didn't see the "?" in your original question. The "?" following either a class for subclass is an indication that the curator is not confident in the call of the class or subclass. As we learn more about the element in question the classification is either changed or the "?" designation is removed.

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06-04-2013, 01:23 AM	#1
rahbz Member Location: Kharagpur, India Join Date: Jun 2013 Posts: 16	help in Repeat Masker Can any of you please let me know the interpretation of the repeat families This is the part of .out file generated by the RepeatMasker 736 26.0 0.6 1.1 chr19 8015 8193 (299) C Eulor5B DNA? (0) 192 15 48785 390 26.9 4.3 10.0 chr19 76047 76220 (93229) C MamRep4096 DNA/hAT? (154) 272 107 48278 390 26.9 4.3 10.0 chr19 76851 76886 (92563) C MamRep4096 DNA/hAT? (320) 106 73 48278 523 25.6 15.0 0.0 chr19 3304 3463 (1384) C MER91A DNA/hAT-Tip100 (11) 185 2 40 268 25.2 4.8 16.2 chr19 6863 6996 (167262) + Charlie7a DNA/hAT-Charlie 1 122 (150) 99 268 25.2 4.8 16.2 chr19 7129 7217 (167041) + Charlie7a DNA/hAT-Charlie 123 203 (69) 99 268 25.2 4.8 16.2 chr19 7459 7527 (166731) + Charlie7a DNA/hAT-Charlie 204 265 (7) 99 What does DNA and DNA? mean What does a question mark indicate at the end of the family. Thank you in advance, Last edited by rahbz; 06-04-2013 at 01:28 AM.

06-11-2013, 11:06 AM	#2
rhubley Member Location: Washington Join Date: Sep 2012 Posts: 10	The "DNA" class stands for DNA Tranposon -- a cut and paste type of interspersed repeats.

06-11-2013, 11:22 PM	#3
rahbz Member Location: Kharagpur, India Join Date: Jun 2013 Posts: 16	Yah but what does 'DNA?' mean what is the difference between 'DNA' and 'DNA?'

06-12-2013, 09:39 AM	#4
rhubley Member Location: Washington Join Date: Sep 2012 Posts: 10	Sorry, I didn't see the "?" in your original question. The "?" following either a class for subclass is an indication that the curator is not confident in the call of the class or subclass. As we learn more about the element in question the classification is either changed or the "?" designation is removed.