Question: Panther Database: how to find start and end position of a Panther ID?
0
gravatar for Chat-ra
14 months ago by
Chat-ra20
Chat-ra20 wrote:

Hello everyone!

I’ve downloaded a file from the Ensembl Biomart here : https://www.ensembl.org/biomart/martview/4cab87e631cda01b9def14f09cc2021f

The chosen database is: “Ensembl Genes 95” and the chosen dataset is “Human Genes (GRCh38.p12)” The chosen attributes are:

  • Gene stable ID
  • Transcript stable ID
  • Protein stable ID
  • hmmpanther ID
  • hmmpanther start
  • hmmpanther end

I’ve access to a start and end position for each Panther ID, same goes with Intepro when I download the last release (protein2ipr.dat.gz) https://www.ebi.ac.uk/interpro/download.html.

My problem is that I can’t seem to find this information in the files provided by Panther DB (http://pantherdb.org/downloads/index.jsp)

Is someone knows where I can find information about the start and end position for a Panther ID?

Thank you for any suggestions!!!

genome • 371 views
ADD COMMENTlink written 14 months ago by Chat-ra20

Are you looking to find the start/stop of where the panther domains map on the protein or which part of the panther domain has been mapped to the protein?

ADD REPLYlink written 14 months ago by lieven.sterck7.8k

I'm looking to find the start/stop of where the panther domains map on the protein

ADD REPLYlink written 14 months ago by Chat-ra20

Did you not mention you have that?

What am I overlooking?

ADD REPLYlink written 14 months ago by lieven.sterck7.8k

I would like to retrieve this information from the Panther database and not a another source in order to assure the validity of the information. I'm sorry if it wasn't clear!

ADD REPLYlink written 14 months ago by Chat-ra20
1

The pantherDB does not work like that. It assigns genes to families from which then HMM are build that can be used to screen 'new' sequences. So a sequence is either part of the certain pantherID or not (== the assignment is always on a complete gene basis).

For a certain pantherID you can look up though which genes are assigned to it. eg. PTHR18929

ADD REPLYlink written 14 months ago by lieven.sterck7.8k

Okey thank you for your help !

ADD REPLYlink written 14 months ago by Chat-ra20
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: 1785 users visited in the last hour