Q:
In Pseudogene.org, the pseudogene datasets of zebrafish (Danio rerio) was based on old annotations (Ensembl 55?). There were about ~1800 processed pseudogenes. However, based on a recent research (http://www.nature.com/nature/journal/v496/n7446/full/nature12111.html), there were rare pseudogenes in zebrafish. (Only 21 processed pseudogenes, according to Supplementary Table 14 in the published manuscript). Is this great conflict due to the old annotations?

A:
This is right, the results were based on an old genome assembly, ENSEMBL release 55, which was done in year 2009. We do notice that the pseudogene number is way too high, which we believe partially due to the quality of the genome assembly, and partially due to the reason that the pipeline parameters were optimized with primates. Given that, for up-to-date pseudogene information in Zebrafish, people should refer to the Nature publication.

Q:
Where is the psiDR file?
A:
The file can be downloaded at: http://www.pseudogene.org/psidr/psiDR.v0.txt

Q:
Is H1-hesc included in the psiDR file?
A:
The chromatin state, promoter prediction and pol2 binding regarding to pseudogenes in H1-hesc are included in the psiDR file.

Q:
Could you let me know briefly how the chromatin states in the psiDR file are determined?
A:
The chromatin states were assessed using the Segway segmentation. Segway annotates the genome using 25 different labels representing active and repressive marks. we use two selection criteria to pinpoint pseudogenes with active chromatin states:
(1) the frequency of the TSS is three times higher than the frequency of any repressive markers;
(2) the gene body start (GS), gene body middle (GM) and gene body end (GE) frequencies are two times larger than the frequency of the repressive markers.
The selection criteria were chosen to match the segmentation behavior of the active genes.

Q:
Why the genomic sequences need to be repeatmasked before their inputs to the pipeline?

A:
This is to block the low complexity regions in genome from pseudogene searching.

Q:
Which database we should use to do the repeatmasking?

A:
Our current pipeline downloads genome data from Ensembl, where the repeats are detected with the RepeatMasker tool. More information about the pseudopipe can be found at: https://faq.gersteinlab.org/category/pseudogenes/.

>
> Dear Prof. Gerstein,
>
> My name is Yiling Lai, a PhD student from Prof. Xingzhong Liu’s > group in Institute of Microbiology, Chinese Academy of Sciences. Our > research focus on comparative genomics of nematode endoparasitic > fungi Hirsutella spp.. Now we start to analyse the genomic sequences > and use the PseudoPipe from your published method to identify > pseudogenes in these genomes. However, some questions confuse us > when we use the pipeline. The first one is why the genomic sequences > need to be repeatmasked before their inputs to the pipeline. The > second question is which database we should use to do the > repeatmasking, the repbase database or database established from de > nove consensus sequences by RepeatScout? We would be very > appreciated if you could give us some good suggestions. Thank you > very much! We’re looking forward for your reply. >
>
> Best wishes
>
>
> Yiling Lai
>
>
> State Key Laboratory of Mycology
>
> Institute of Microbiology
>
> Chinese Academy of Sciences
>
> No.3 1st Beichen West Road, Chaoyang District
>
> Beijing 100101, PR China