Detect Repeats

The DetectRepeats function can find tandem or interspersed repeats in gene, protein, or genome sequences.

For an in-depth tutorial on DetectRepeats, see the "Detecting Obscure Tandem Repeats in Sequences" vignette, available from the Documentation page.

How do I detect tandem repeats?

First it is necessary to install DECIPHER and load the library in R. Next, upload sequences and run DetectRepeats to identify any tandem repeats.

Hide output

library(DECIPHER)
> options(width=50)
> 
> # load the DECIPHER library in R
> library(DECIPHER)
> 
> # specify the path to the FASTA file (in quotes)
> fas <- "<<REPLACE WITH PATH TO FASTA FILE>>"
> 
> # load the sequences from the file
> # change "DNA" to "RNA" or "AA" as needed
> seqs <- readDNAStringSet(fas)
> 
> # look at some of the sequences (optional)
> seqs
DNAStringSet object of length 11:
      width seq               names               
 [1] 107976 ATGACAA...CATTTAA titin isoform IC
 [2]  26778 ATGGATC...GCGCTGA obscurin isoform c
 [3]  16908 ATGATTT...ATACTAA hemicentin-1 prec...
 [4]   5847 ATGGCGC...AACCTAA receptor-type tyr...
 [5]   5745 ATGGGGG...AGAGTGA myosin light chai...
 ...    ... ...
 [7]   3825 ATGCCTG...TCAGTGA myosin-binding pr...
 [8]   1497 ATGTTTA...ACTTTAA myotilin isoform a
 [9]   1263 ATGCTCA...CCTCTGA mannose-1-phospha...
[10]   1101 ATGGTGC...TATCTAA inhibin alpha cha...
[11]    717 ATGTCTA...GGCCTGA SPEG neighbor pro...
> 
> # detect tandem repeats
> TRs <- DetectRepeats(seqs)
  |========================================| 100%


Time difference of 68.85 secs


> 
> # view the first tandem repeats
> head(TRs)
  Index Begin   End         Left        Right
1     1   844   972 844, 865.... 864, 897....
2     1  1287  2114 1287, 14.... 1436, 15....
3     1  4232  4332 4232, 42.... 4246, 42....
4     1  8390  9719 8390, 86.... 8650, 89....
5     1 16194 17591 16194, 1.... 16472, 1....
6     1 24926 28615 24926, 2.... 25213, 2....
     Score
1 21.46971
2 81.77987
3 39.66848
4 33.95958
5 25.50887
6 37.54636
> 
> # view the last tandem repeats
> tail(TRs)
   Index Begin   End         Left        Right
19     2 24506 24589 24506, 24548 24547, 24589
20     3  5500 12591 5500, 57.... 5781, 60....
21     3 13581 14606 13581, 1.... 13751, 1....
22     3 15270 15644 15270, 1.... 15389, 1....
23     5  2677  2844   2677, 2761   2760, 2844
24     5  3037  3234 3037, 30.... 3072, 31....
       Score
19  10.95497
20 250.98565
21  82.65828
22  16.39137
23  15.51914
24  45.80374
> 
> # see the help page for more examples
> ?DetectRepeats