How to visualize repeated subsequences in a genome?

Question

[thustar]

Hi biostars!

I would like to visualize all repeated subsequences in a bacterial genome which might contain several million bases. Is there any software to do this task?

Thanks in advance.

[GenoMax]

You could try doing dot plots as a simple analysis first. While you could try doing one across the genome it may be better to do smaller sections first.

Answer 1

[natasha.sernova]

REPuter - this is a program for it. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC55324/

It's not alone.

There are a lot of tools mentioned here:

http://molbiol-tools.ca/Genomics.htm

These tools are not only for bacteria, but sometimes they are suitable for plants and visa versa, for example.

https://www.researchgate.net/publication/221871734_Tandem_repeat_markers_as_novel_diagnostic_tools_for_high_resolution_fingerprinting_of_Wolbachia_Review

MLVA as well may be used: http://www.mlva.net/

[thustar]

Thank you. Lots of information you provide