[maker-devel] Pseudogene identification

[Quanwei Zhang]

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
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20170801/14e6d16f/attachment-0002.html>