RepeatMasker-help

[bioman1]

I would like to use repeatmasker to identify repetitive element in my de novo assembled genome. I have installed repeatmasker with repbase database in my local server.

My de novo assembled genome is plant fruit crop which is tetraploid crop. It is non-model plant and I don't know which is the nearest clad belong to my genome.

can I use arabidopsis database in repeat masker to find repeats with default settings? Is this correct way to do this?

Below is the running command of repeatmasker

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RepeatMasker my.contigs.fa -species arabidopsis
RepeatMasker version open-4.0.5
Search Engine: Crossmatch [ 1.080812 ]
Master RepeatMasker Database: path/RepeatMaskerLib.embl ( Complete Database: 20140131 )


Building species libraries in: /path/.RepeatMaskerCache/20140131/arabidopsis
- 176 ancestral and ubiquitous sequence(s) for arabidopsis
- 524 lineage specific sequence(s) for arabidopsis

[WhatsOEver]

1) On the Repeatmasker webserver, you can choose also Triticae or Panicoid. I think these are more appropriate in your case
2) I would like to suggest using RepeatModeler, instead of RepeatMasker alone (http://www.repeatmasker.org/RepeatModeler.html). The installation takes some time, but besides Repeatmasker, it uses Recon, Repeatscout and TRF to identify and classify repetitive sequences.
3) Depending on how complete your analysis on repetitive sequence should become, I can further suggest MISA for the identification of SSRs (http://pgrc.ipk-gatersleben.de/misa/)