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.

Instructions

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