[maker-devel] Repeats...

[Panos Ioannidis]

An additional question related to the previous.

I searched my species-specific repeat library with InterProScan and can't
find a single sequence with similarity to a transposable element...

I would expect it to find at least a few transposases. Is there an
explanation for this, or has something gone wrong?

Thanks,
P


On Fri, Jul 10, 2015 at 11:50 AM, Panos Ioannidis <panos.ioannidis at gmail.com
> wrote:

> Hi guys,
>
> I have finished running Maker on my genome, but get >800 genes (out of
> ~20,000) that have similarity to transposases. Except from RepBase, have
> also built a species-specific repeat library, so it's weird that I still
> have quite a few transposases in my gene set...
>
> The repeat masking-related parameters in my maker-opts.ctl file are:
>
> model_org=all #select a model organism for RepBase masking in RepeatMasker
> rmlib=consensi.fa.classified #provide an organism specific repeat library
> in fasta format for RepeatMasker
> repeat_protein=/Home/pioannid/Programs/maker/data/te_proteins.fasta
> #provide a fasta file of transposable element proteins for RepeatRunner
> rm_gff= #pre-identified repeat elements from an external GFF3 file
> prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change
> this), 1 = yes, 0 = no
> softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg
> and dust filtering)
>
> Does anyone have an idea why I'm getting so many transposases?
>
> Thanks,
> Panos
>
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