how to find consensus sequence for repeats
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0
Entering edit mode
6.1 years ago
dli ▴ 240

Hi,

I downloaded the rmsk.txt from UCSC genome browser, http://genome.ucsc.edu/cgi-bin/hgTables?db=hg38&hgta_group=rep&hgta_track=rmsk&hgta_table=rmsk&hgta_doSchema=describe+table+schema,

I got following stuff:

bin swScore milliDiv    milliDel    milliIns    genoName    genoStart   genoEnd genoLeft    strand  repName repClass    repFamily   repStart    repEnd  repLeft id
585 463 13  6   17  chr1    10000   10468   -248945954  +   (TAACCC)n   Simple_repeat   Simple_repeat   1   471 0   1
585 3612    114 215 13  chr1    10468   11447   -248944975  -   TAR1    Satellite   telo    -399    1712    483 2
585 484 251 132 0   chr1    11504   11675   -248944747  -   L1MC5a  LINE    L1  -2382   395 199 3
585 239 294 19  10  chr1    11677   11780   -248944642  -   MER5B   DNA hAT-Charlie -74 104 1   4
585 318 230 37  0   chr1    15264   15355   -248941067  -   MIR3    SINE    MIR -119    143 49  5
585 18  232 0   19  chr1    15797   15849   -248940573  +   (TGCTCC)n   Simple_repeat   Simple_repeat   1   52  0   6
585 18  137 0   0   chr1    16712   16744   -248939678  +   (TGG)n  Simple_repeat   Simple_repeat   1   32  0   7
585 239 338 129 0   chr1    18906   19048   -248937374  +   L2a LINE    L2  2942    3104    -322    8
585 994 312 60  25  chr1    19971   20405   -248936017  +   L3  LINE    CR1 2680    3129    -970    9
585 270 331 7   27  chr1    20530   20679   -248935743  +   Plat_L3 LINE    CR1 2802    2947    -639    1

For example, the repeat name L1MC5a, if I want to get the sequence of this repeat, should I found from RepBase? But I could not find it from Repbase: http://www.girinst.org/repbase/update/browse.php?type=All&format=EMBL&autonomous=on&nonautonomous=on&simple=on&division=Homo+sapiens&letter=L

Aanyone has suggestions on how to fix this? Thanks a lot in advance.

genome repeat • 2.0k views
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6.1 years ago
GenoMax 115k

See if table browser @UCSC works.
Select human(?) genome --> Group (Repeats) --> Track (Repeatmasker) --> Region (whole genome/region?) --> Output format (Sequence) --> Give a file name to save the data to file.

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Thanks for you reply @genomax2.

I am not actually looking for genomic sequence for copies, I am looking for consensus sequences.

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I don't think there is a consensus. The repeats by their nature will have difference. e.g. If I restrict to the output to L2a LINE repeat I get this summary from the table browser

item count  174,058
item bases  43,353,715 (1.42%)
item total  43,373,283 (1.42%)
smallest item   11
average item    249
biggest item    3,283
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