Unitary Pseudogene PROMOTER

Q:
I am trying to find an example of a unitary pseudogene whose
promoter is known to be mutated as well and therefore the gene is
definitely non-functional. I can find articles stating there are many
examples of unitary pseudogenes in humans (e.g. Vitamin C) but none
seem to mention the promoter. Any thoughts?

A:
Our analyses compiled a number of activity features associated with pseudogenes (e.g. transcription, presence of functional Pol2 and TF binding sites in the upstream region, presence of open chromatin) that are available in online. Please see https://www.ncbi.nlm.nih.gov/pubmed/22951037 (http://pseudogene.org/psidr/ ) and https://www.ncbi.nlm.nih.gov/pubmed/25157146 (http://pseudogene.org/psicube/) for the functional characterisation of pseudogenes. In particular the unitary pseudogenes that do not have transcription, Pol2 and TF binding sites should be the ones to look at and to check the conservation or not of the promoter region.

Zebrafish pseudogenes

Q:
I have a question regarding Zebrafish pseudogenes. I searched few
zebrafish genes to check if they have any pseudogenes existing in the
pseudogene.org, I found that there are 15779 zebrafish pseudogenes.
But when I read the nature reference that you mentioned in your blog
has total 154 zebrafish pseudogenes! Could you please let me know how
can one see those 154 pseudogenes, if I want to know whether my genes
of interest having pseudogenes or not?

A:
Pseudogene.org provides a set of pseudogenes resulted from automatic annotation. Zebrafish is a peculiar genome. It was subjected to numerous large scale genome duplication and thus is full of repeats. As such the automatic annotation overstates the number of pseudogenes present. We followed up the automatic annotation with manual curation that resulted in a subsequent much smaller number of pseudogenes. The continuous improvements in the genome annotation result in further improvements in pseudogenes annotation. I attach here the latest set of zebrafish pseudogenes.

problem in PseudoPipe

Q:
I tried to run the software PseudoPipe
(http://pseudogene.org/DOWNLOADS/pipeline_codes/ppipe.tar.gz) using the
example as following:
./pseudopipe.sh ~/bin/pgenes/ppipe_output/caenorhabditis_elegans_62_220a
~/bin/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/dna_rm.fa
/home/liuhui/bin/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/Caenorhabditis_elegans.WS220.62.dna.chromosome.%s.fa
~/bin/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/pep/Caenorhabditis_elegans.WS220.62.pep.fa
/home/liuhui/bin/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/mysql/chr%s_exLocs
0

And I got the output in the attachment and attfollowing lines in the screen:
Making directories
Copying sequences
Fomatting the DNAs
Preparing the blast jobs
Finished blast
Processing blast output
Finished processing blast output
Running Pseudopipe on both strands
Working on M strand
sh: 1: source: Permission denied
Finished Pseudopipe on strand M
Working on P strand
sh: 1: source: Permission denied
Finished Pseudopipe on strand P
Generating final results
find:
`/home/liuhui/bin/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/pgenes/minus/pgenes’:
No such file or directory
find:
`/home/liuhui/bin/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/pgenes/plus/pgenes’:
No such file or directory
gzip:
/home/liuhui/bin/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/pgenes/*/pgenes/*.all.fa:
No such file or directory
Finished generating pgene full alignment
Finished running Pseudopipe

Could you please help me in solving the problem?

A:
Looks like you have permission problems. The script tries to source the file setenvPipelineVars that you will find in /home/liuhui/bin/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/pgenes/minus and /home/liuhui/bin/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/pgenes/plus . If you open that file you’ll see a couple of export functions and from the look of it I would guess that you do not have rights to export to the Path. So I suggest you get admin rights and run as root.

pseudogene.org error message

Q:
I would just like to bring the below error message to your attention that I recently received when attempting to access data on pseudogenes.org. (see image)

A:
We were not able to reproduce your error. In order to understand what happened and find a solution, it would be of a considerable help if you could let us know the exact commands you made that resulted in this error.

Question re rice pseudogene

Q:
I am using your pseudogene dataset of rice to do some analysis. However, I found that you did not mention which Rice genome version you used for data analysis, so I cannot anchor the pseudogenes to the genome I used. Would you please give the information.

A:
As I understand you are using the pseudogenes described in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2708354/ . The Data source section of the paper highlights the fact that the annotations were done on the Rice genome version 5 from TIGR. You can find all the information regarding the rice genome version 5 at ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa .