[maker-devel] repeat masking and repeat libraries

[Michael Campbell]

Hi Xabier,

>From what you described I would leave it as is.

Mike

On Wed, Jan 21, 2015 at 5:42 PM, Xabier Vázquez Campos <xvazquezc at gmail.com>
wrote:

> 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
>>>  _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>>
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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
>



-- 
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
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