[maker-devel] Pseudogene identification

[Quanwei Zhang]

Dear Carson:

Thanks again for all your previous help. I am still trying to identify
pseudo genes. For me, I have two goals to identify pseudo genes.
(1) Check which predicted protein coding genes are in fact pseudo genes
(especially I want to check genes belong to gene families, which are found
under expansion in our analyzed geome).
(2) Identify pseudo genes in the intergentic regions.
But the link "
http://shiulab.plantbiology.msu.edu/index.php/Protocol:Pseudogene" only
describe Identification of pseudo genes in the intergentic regions. I
wonder whether I can simple follow the pipeline and run it on the whole
genome, so I can achieve my two goals above. Or do I need to do some
adjustment of the pipeline?

At beginning, I though the pipeline is only useful to identify pseudo genes
in the intergentic regions, but in the following paper, they mentioned the
pipeline was applied to the whole genome. So I think maybe I can also do
this, but not sure whether I can simply run the same pipeline in the
following link on whole genome ("
http://shiulab.plantbiology.msu.edu/index.php/Protocol:Pseudogene").

In the paper "MAKER-P: A Tool Kit for the Rapid Creation,Management, and
Quality Control of Plant Genome Annotations". It saids "If the analysis
pipeline is applied to the whole genome, 2.5% and 0.6% of currently
annotated proteincoding genes are identified as pseudogenes due to the
presence of misidentified stops and frame shifts, respectively, indicating
that the false-positive rate of our pipeline is 3.1%."

Many thanks for your help.

Best
Quanwei


2017-08-01 9:32 GMT-04:00 Quanwei Zhang <qwzhang0601 at gmail.com>:

> Hi Carson:
>
> I took a look at the description about the pipe line of pseudogene
> identification. In my understanding it will use the annotated (predicted by
> Maker2) protein coding genes as input (i.e., query sequences), search in
> the intergenic spaces (so annotated genes will not be checked) and find the
> regions where show certain level of similarity to the annotated genes.
>
> If my understanding is correct, I think it is not what I want to do get.
> Based on the annotated coding genes from Maker2, we found some genes are
> under expansion in the new species. We want to check and make sure all the
> gene copies in the expanded gene family really function (to make sure they
> are not pseudogenes).
>
> Do you think the pseudogene identification pipe line of Maker2 can be
> helpful for my goal? Or do you have any suggestions on this?
>
> Many thanks
>
> Best
> Quanwei
>
> 2017-07-31 19:54 GMT-04:00 Carson Holt <carsonhh at gmail.com>:
>
>> The MAKER-P fork was merged back into standard MAKER with version 2.29
>> (roughly 3 years ago - a separate download no longer exists). This is
>> because MAKER-P’s functionality is almost entirely in accessory scripts and
>> written protocols. The …/maker/bin/maker called by both MAKER2 and MAKER-P
>> is actually the same script. So no need to rerun, because if you are using
>> version 2.29 or later, you already ran it.
>>
>> Pseudogene calling is therefore handled by accessory scripts and
>> protocols you can find here —> http://shiulab.plantbiology
>> .msu.edu/wiki/index.php/Protocol:Pseudogene
>>
>> The other MAKER-P protocols can be found here —>
>> http://www.yandell-lab.org/software/maker-p.html
>>
>> --Carson
>>
>>
>>
>> On Jul 31, 2017, at 5:02 PM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
>>
>> Hello:
>>
>> We used Maker2 to annotate a new rodent genome. By using the annotated
>> genes we did gene family expansion analysis, and found several gene
>> families under expansion in the new rodent genome. But we want to check
>> whether some annotated genes are Pseudogenes, which lead to the expansion.
>> Do you have any suggestions on this?
>>
>> We found the Maker-P can annotate Pseudogene, but we are not sure whether
>> it is worth to repeat our annotation with Maker-P. Besides, we are not sure
>> whether the default parameters of Maker-P are good for a rodent species.
>> What's more, in my understanding the Maker-P will identify Pseudogenes in
>> the intergenic spaces (which I think the annotated coding genes will be not
>> be tested and checked).
>>
>> Do you have any suggestions to solve our problem? We do not want to
>> identify Pseudogene on the genome wide, but only want to check those genes
>> showing expansion (to make sure all those gene copies really function).
>>
>> Many thanks
>>
>> Best
>> Quanwei
>>
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>>
>>
>
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