Is There Is Tool For Variable Tandem Repeats Finding?

Question

[zeleniy.spb]

For example I have the next sequence:

ACGAGGTTACTACTACTAGTACTACGCC
#      _________^^^______

As you can see there is a tandem repeat with monomer TAC. But because of mutation one monomer now is TAG and, for example, exact-tandems tool cannot recognise TACTACTACTAGTACTAC as one repeat. So how can I identify TACTACTACTAGTACTAC as one repeat, not two separated by TAG sequence?

Answer 1

[Medhat]

NTRFinder: a software tool to find nested tandem repeats

and here is a review Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance.

Answer 2

[JC]

Try the old and still working Tandem Repeat Finder http://tandem.bu.edu/trf/trf.html

[Elke Schaper]

The common reason to use TRF is that has been used by a lot of other researchers, and is well cited. However, benchmarks show that it lacks sensitivity, without being particularly specific. Thus, I'd recommend using other tools, or at least adding results from other tools.

Answer 3

[Elke Schaper]

Quite a lot of reviews have been published on the topic. Have a look at e.g.

Detecting short tandem repeats from genome data: opening the software black box

Repeat or not repeat?- Statistical validation of tandem repeat prediction in genomic sequences

Among many more tools (>50), there is:

XSTREAM

T-REKS

Perhaps useful, we've implemented the Python3 library TRAL to allow among others easy running, parsing and merging of tandem repeat detection tools.

Answer 4

[kashiff007]

See also, MEME-suite (http://meme-suite.org/doc/meme-format.html). It's different tools by which you can discover new repeats (MEME), can look for repeat/motif enrichment in particular region of the genome (CentrMo), can scan your repeat/motif in the genome (FIMO) and many more related analysis.

Answer 5

[Jordan]

Why don't you take a look at EMBOSS etandem? And here is the manual -> link

Answer 6

[Sukhi Singh]

Also, check out MISA

Beier S, Thiel T, Münch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33 2583–2585. dx.doi.org/10.1093/bioinformatics/btx198