About Repeatmasker

Question

[Zhshqzyc]

Hello,

I have a nucleotide sequence(fasta format) size limit of 20 kb. And also I have my own genome sequence file(repeat database, also fasta format, 200GB) on my local machine. I want to identify repetitive elements in genome sequence.

Questions: 1)Which software is best? I heard about RepeatMasker. 2)If RepeatMasker will be used, what kind of format for repeat library? I mean do I convert fasta format to some sort of format? 3)What is low-complexity DNA sequences and interspersed repeats?(off topic of course, you don't have to answer it)

Thanks.

[Casey Bergman]

please read the repeat masker help pages and see if this answers your question: http://www.repeatmasker.org/webrepeatmaskerhelp.html

[Zhshqzyc]

Partly, I still don't know the format of Reference repeat databases. Is a huge fasta file okay?

Answer 1

[Elizabeth]

Hi,

First of all, with what purpose do you want to identify repetitive elements in your genome sequence?

If you are just interested in masking them from the genome, I would use RepeatMasker with a repeat database from RepBase www.girinst.org, yes fasta format is OK) to mask transposable elements by similarity to already described transposons. To identify tandem repeats (typically minisatellites, repeated motifs of 20-50 nuclotides) you can use TRF (http://tandem.bu.edu/trf/trf.html). TANTAN also identifies tandem repeats, and low-complexity sequences as well (ATATAT for example) (http://www.cbrc.jp/tantan/)

If what you are interested in is identifying and classifying transposable elements in your genome, there are various tools to identify different types of transposons, but that calls for a longer mail... let me know if its the case.

Cheers,

Elizabeth