[maker-devel] repeat masking and repeat libraries

[Xabier Vázquez Campos]

Thanks Mike,

I've blasted (blastx against nr) and many, if not most of the repeatmodeler
library sequences match with transposases, pol proteins, gag proteins,
retrotransposons,... all of them present in other fungi of the same order.
Should I leave it to be masked? I still do run prediction on the unmasked
genome too?
Also, in many cases, the match a couple of thousand bp on the extreme of a
9kbp sequence and in none of them InterProScan is capable of finding
anything except potential TM domains or so, provided by SignalP.

What do you think? Should I leave it as it is?

Thank you again for your time

2015-01-17 4:08 GMT+11:00 Michael Campbell <michael.s.campbell1 at gmail.com>:

> Hi Xabier,
>
> I haven't seen orders or families documented for repeatmasker with
> repbase. Fungi seems safe to me.
>
> If you want to give yourself a little more peace of mind about the
> repeatmodeler library you can blast it to database of known fungal proteins
> and remove the entries int he library that have strong hits to a known
> protein to avoid over-masking.
>
> Mike
>
> On Fri, Jan 16, 2015 at 10:04 AM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Using both RepBase and a RepeatModeler produced library should be
>> sufficient, especially for fungi.
>>
>> —Carson
>>
>>
>> On Jan 16, 2015, at 3:11 AM, Xabier Vázquez Campos <xvazquezc at gmail.com>
>> wrote:
>>
>> Hi there,
>>
>> First, a general question. Probably kind of silly but I prefer to be
>> sure... When you browse RepBase, for example in fungi, all the repeats are
>> marked as Eukaryota (Ancestral) or under the name of the species but no
>> other taxa ranks are indicated. Does RepeatMasker recognise orders,
>> families etc? or in my case should I stick with model_org=fungi?
>>
>> I've been trying to create a repeat libraries specific for my genomes and
>> I did't have any luck with the programs described in the Basic
>> <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction--Basic>
>> and advanced
>> <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction--Advanced>
>> tutorials (neither in my computer or in the cluster), reporting errors at
>> all times, with exception of RepeatModeler, which ran with no problems. Is
>> the output from RepeatModeler enough to improve the masking? It is not the
>> best option I guess, but better than just the RepBase libraries by
>> themselves, isn't it?
>>
>> Thank you for your time,
>>
>> Xabier
>>
>> --
>> Xabier Vázquez Campos
>> *PhD Candidate*
>> Water Research Centre
>> School of Civil and Environmental Engineering
>> The University of New South Wales
>> Sydney NSW 2052 AUSTRALIA
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>>
>>
>>
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>>
>
>
> --
> Michael Campbell MS, RD.
> Doctoral Candidate
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> ph:585-3543
>
>


-- 
Xabier Vázquez Campos
*PhD Candidate*
Water Research Centre
School of Civil and Environmental Engineering
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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