Ref Genome Repeat Masker

[kwebb]

I am looking for a tool that will mask (replace with X's) regions of the reference genome that occur multiple times. So something along the lines of BLASTing the reference genome to itself, identifying regions of a given length or longer that are identical or highly identical due to multiple occurrences within the reference genome, and then replacing those positions with X's. Does anyone know of this tool?

I've collected 36 and 40 bp short reads for a eukaryotic genome that is not yet published or annotated but I do have access to contigs and super contigs. Being able to assemble to only the unique regions will simplify our analyses.

Thanks for your help.

[kmcarr]

RepeatMasker

http://www.repeatmasker.org/

[kwebb]

Thanks.

I've looked into RepeatMasker and it appears that I have to pay for a license for either Cross_Match, ABBLast/WUBlast or DeCypher? I'm at a government lab. Is there a free work around or another tool that you know of?

[whsqwghlm]

vmatch can be used to find repetitive sequences in a genome, but does not classify them for you.

[ewingad]

Give P-clouds a try: http://www.evolutionarygenomics.com/PClouds.html

[Thomas Doktor]

If you supply the repeat regions in a BED file, BEDTools can mask the fasta sequences for you.

[robsyme]

You don't have to pay for crossmatch. If you email the people at Washington, they send you out an academic copy if you put your name to the licence agreement.
-r