coordinates of pfam domains in mouse
16 views
Skip to first unread message
Brian White
Dec 1, 2015, 12:10:14 PM12/1/15
to gen...@soe.ucsc.edu
Hello,
I would like a list of pfam domains with their mappings to mm9.
Such functionality seems to be provided for hg19 in the Pfam in UCSC
gene track,
as described here
http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=10689&S=e142e3f6ebbe77412ce70628d6509d9a
And I see that I can a list of pfams domains in a gene in mouse, as
described here:
http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=11282&S=5f4f3998247f8a15ca208f990c3dbe09
But the latter seems to return the coordinates of the gene, not the
coordinates of the domain
within the gene.
Is there a solution for mouse?
Thank you,
Brian
--
Brian White, PhD
Assistant Professor
Department of Medicine, Oncology Division / McDonnell Genome Institute
Washington University School of Medicine
____
This email message is a private communication. The information transmitted, including attachments, is intended only for the person or entity to which it is addressed and may contain confidential, privileged, and/or proprietary material. Any review, duplication, retransmission, distribution, or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is unauthorized by the sender and is prohibited. If you have received this message in error, please contact the sender immediately by return email and delete the original message from all computer systems. Thank you.
I would like a list of pfam domains with their mappings to mm9.
Such functionality seems to be provided for hg19 in the Pfam in UCSC
gene track,
as described here
http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=10689&S=e142e3f6ebbe77412ce70628d6509d9a
And I see that I can a list of pfams domains in a gene in mouse, as
described here:
http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=11282&S=5f4f3998247f8a15ca208f990c3dbe09
But the latter seems to return the coordinates of the gene, not the
coordinates of the domain
within the gene.
Is there a solution for mouse?
Thank you,
Brian
--
Brian White, PhD
Assistant Professor
Department of Medicine, Oncology Division / McDonnell Genome Institute
Washington University School of Medicine
____
This email message is a private communication. The information transmitted, including attachments, is intended only for the person or entity to which it is addressed and may contain confidential, privileged, and/or proprietary material. Any review, duplication, retransmission, distribution, or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is unauthorized by the sender and is prohibited. If you have received this message in error, please contact the sender immediately by return email and delete the original message from all computer systems. Thank you.
Luvina Guruvadoo
Dec 8, 2015, 4:50:35 PM12/8/15
to Brian White, gen...@soe.ucsc.edu
Hello Brian,
Thank you for your question. One of our engineers has created a Pfam in UCSC Genes track for our mm9 assembly. It will be available on our preview server after this Friday: http://genome-preview.ucsc.edu. However, please be aware that our preview site contains a lot of experimental and
untested data and may undergo changes.
If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
--
Reply all
Reply to author
Forward
0 new messages