In search of best tool for finding repeats

Question

[Fazal]

Hi everyone. I am in need of a best tool for finding Direct repeats (not tendem repeats) in a fungus whole genome whose sequence is available through NCBI. I don't need neither to compare it with library nor create my own that's used in repeatmasker and recon etc. I need a tool that can give the output telling that this sequence(repeat) is present whether 3 times or more (frequncy) giving the position of bp in original sequence. I am using Repeat extraction (http://bioserver2.physics.iisc.ernet.in/RepEx/) but facing technical issues while getting the results for option of direct repeats. can anyone help me in this regard? Thanks in advance for your suggestions and comments. Fazal Sattar

Answer 1

[Lars Juhl Jensen]

If you are looking for the same sequence of, e.g., at least length 10 that is perfectly repeated at least 3 times with no spacer, you can do that with a regular expression:

(.{10,})\1\1

All you have to do is write a simple script in a language of your choice that searches for matches to this regular expression.