Software like REPuter

[Antony03]

Hi,

Do you know a free software like REPuter for find and visualise repeat sequences?
Thanks

[SES]

By repeat structures, I assume you mean transposable elements? If so, there are more sophisticated programs to predict both Class I and Class II TEs based on structure and domain architecture. Tell us what you want to find so that we can make suggestions. The general topic of repeat finding is so broad that it would be hard to start listing programs without a better idea of what you are trying to do. Also, the visualization offered by that program is pretty crude. What type of visualization did you have in mind?

[Antony03]

Hi!
I'm working on de novo chloroplast genome, and there are a lot of little repeated sequences.
For exemple, REPuter can find all little repeated sequences who have more than 30 nucleotid. This is an output example:

>Sequence1
tcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtatt
>Sequence2
tcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtatt
>Sequence3
tcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtatt
>Sequence4
tcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtatt
>Sequence5
tcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtatt
>Sequence6
tcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtatt
>Sequence7
tcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtatt
>Sequence8
aggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagagga
>Sequence9
tcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtatt
>Sequence10
aggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagagga
>Sequence11
tcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtatt
>Sequence12
aggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagagga
>Sequence13
aggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagagga
>Sequence14
tcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtatt
>Sequence15
aggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagag
>Sequence16
aggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagaggatgagcatagcgaatactcgtcagagga
>Sequence17
aggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagaggaacttctcgaccgtatgggagag
>Sequence18
tcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtattacatgcgtagcatgtattcctctcattcttcgagtatt
>Sequence19

There are other kind of output file. After, I can use REPEATmasker for mask all repeated sequences in my genome and know what is pourcentage of it. What I mean by ''visualise'', it's the density of repeated sequences, for exemple:

http://t1.gstatic.com/images?q=tbn:ANd9GcT-XPjKUuut_09vH0YLHzNkZxhJtPwFvevICdAyPkrP6ZDXF8fmO8LizSEu

Thanks!

[SES]

There are no transposable elements in the chloroplast genome, but there are large (and probably numerous small) tandem repeats. One idea would be to just calculate the density of repeats across the genome and plot that as a histogram. I have done this for looking at the tandem repeats in chloroplast genomes.

[Antony03]

Thanks for you answer! Do you know a software for do this?

[SES]

Thanks for you answer! Do you know a software for do this?

You could use TRF or Vmatch or any number of tools to find the repeats. From there it may take a little scripting so you can plot the repeat density in R (or any other plotting program).