Question: Finding the parent gene of pseudogene in mouse
0
gravatar for pyKey
13 months ago by
pyKey30
pyKey30 wrote:

Hello everybody,

I have a list of ENSEMBLE mouse genes and I wnat to investigate if some of the pseudogenes are mutations of some genes, for example: if 'ENSMUSG00000084349' has been extracted from 'ENSMUSG00000060036'. Is there any systematic structure to check this?

Thank you very much,

genomics pseudogene genome • 482 views
ADD COMMENTlink modified 13 months ago by Juke-341.2k • written 13 months ago by pyKey30
1
gravatar for Juke-34
13 months ago by
Juke-341.2k
Sweden
Juke-341.2k wrote:

Catch all genes similar to your pseudogene using blast, then perform an alignment with all the sequences, your pseudogene sequence included ; then create a phylogenetic tree. The closest sequence to your pseudogene Will probably be the parental sequence.

ADD COMMENTlink written 13 months ago by Juke-341.2k
0
gravatar for Juke-34
13 months ago by
Juke-341.2k
Sweden
Juke-341.2k wrote:

Hello,

To check this kind of assumption I guess using a phylogeny approach would be one of the best way.

ADD COMMENTlink written 13 months ago by Juke-341.2k

Hi Juke, if I want to find the parent gene of lots of pseudogenes using phylogeny method, is it acceptable using some simple method to infer the relations of sequences, such as a NJ tree? The ML tree needs a lot of computing resources. Comparing with a rigorous blast search (perform a blast search to find the parent gene of pseudogene using rigorous filters), is the NJ tree method more accurate?

ADD REPLYlink written 6 months ago by niuyw20

I would definitely prefer to use ML tree if I had the possibility. And between NJ tree and rigorous Blast, I will turn without hesitation to the NJ tree.

ADD REPLYlink written 6 months ago by Juke-341.2k

Thanks, Juke. It is very helpful.

ADD REPLYlink written 6 months ago by niuyw20
0
gravatar for pyKey
13 months ago by
pyKey30
pyKey30 wrote:

Thank you!

Could you elaborate a bit? Are there any published hierarchical information out there? Sorry I am not from bioinfo background :)

ADD COMMENTlink written 13 months ago by pyKey30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 462 users visited in the last hour