hg38 RepeatMasker v4.0.7 Dfam_2.0 question
Zhao, Yiyong
Dear UCSC Genome Browser Support Team:
I hope this message finds you well.
I am writing to you as a postdoctoral researcher from Dr. Xianjun Dong's Lab at Harvard Medical School. Firstly, I would like to extend my heartfelt gratitude for your significant efforts in developing the human genome TE annotation. Your work is greatly appreciated and is of immense value to the research community.
Recently, I have encountered a query regarding the hg38 RepeatMasker v4.0.7 Dfam_2.0 in the UCSC genome browser, which I believe you might be able to shed some light on.
It appears that the most updated TE annotation file was annotated using a consensus sequences library from Dfam 2.0 by RepeatMasker. However, I have noticed a discrepancy: I am unable to find matching TE subfamily information between the hg38 RepeatMasker v4.0.7 Dfam_2.0.gtf and the DfamConsensus.embl from the RepeatMasker-4.0.7 Library.
Specifically, I am curious about why the 182 LINE subfamily/clade names (as identified by Kenji K. Kojima, 2018, in Mobile DNA) included in the hg38 RepeatMasker v4.0.7 Dfam_2.0.gtf do seem to correspond with the LINE classifications in the Repbase database. Could you provide some insight into the relationship between the hg38 RepeatMasker v4.0.7 Dfam_2.0.gtf and the Repbase database? Or how this hg38 RepeatMasker v4.0.7 Dfam_2.0 was generated.
I would greatly appreciate any assistance or guidance you could offer in resolving this query. Your expertise in this matter would be invaluable to my ongoing research.
Thank you very much for your time and consideration. I look forward to your response.
Best regards,
Yiyong(Rambo) Zhao, PhD
Genomics and Bioinformatics Hub
Harvard Medical School/Brigham and Women’s Hospital
TEL: +18573815442
From:
Dong, Xianjun <xdo...@bwh.harvard.edu>
Date: Tuesday, November 21, 2023 at 17:26
To: subscriptions - PB <subscr...@phoenixbioinformatics.org>
Cc: Zhao, Yiyong <yz...@bwh.harvard.edu>, zachary...@phxbio.org <zachary...@phxbio.org>
Subject: Re: Assistance Required for Completing Institutional Subscription Application for Repbase [ ref:!00Do00J6b5.!500QU026CQM:ref ]
HI Zachary,
Here is Rambo’s supervisor. Thanks for your help on Rambo re Repbase subscription. Looking forward to hearing from your followup with Harvard lib staff.
Thanks a lot,
Xianjun Dong, PhD
——————————————————————————
Director, Genomics and Bioinformatics Hub
Director of Computational Neuroscience, Precision Neurology Program
APDA Center for Advanced Parkinson Research
Brigham and Women's Hospital
Assistant Professor in Neurology, Harvard Medical School
Associate Member, Broad Institute
Faculty Member, Harvard Initiative of RNA Medicine
Building for Transformative Medicine,
60 Fenwood Road, 9002R
Boston, MA 02115
Tel: +1-857-307-5423
Fax: +1-857-307-5476
Lab website: http://donglab.org
On Nov 21, 2023, at 5:20 PM, subscriptions - PB <subscr...@phoenixbioinformatics.org> wrote:
External Email - Use Caution
Hello Rambo,
I would like to follow up on my email from November 17th and ask if you received it? We experienced issues with our email server resulting in emails not being properly sent and received. Please let me know otherwise.
Thank you,Zachary Zouyed
Sales Support Representative
--------------- Original Message ---------------
From: subscriptions - PB [subscr...@phoenixbioinformatics.org]
Sent: 11/17/2023 2:46 PM
To: yz...@bwh.harvard.edu; xdo...@bwh.harvard.edu
Subject: RE: Fwd: Fwd: Assistance Required for Completing Institutional Subscription Application for Rebase [ ref:!00Do00J6b5.!500QU026CQM:ref ]
Hello Rambo,
Thank you for reaching out and apologies for the delayed response as I was traveling back home. I would be more than happy to assist you with your request! Before proceeding, I would like to contact the Harvard University library staff. Harvard University is already subscribed to Repbase and since Brigham and Women’s Hospital is associated with Harvard Medical School we may be able to provide access through the primary colleges subscription.
Please allow two to three business days for me to reach out. I will follow up as soon as I receive a response! I appreciate your patience and look forward to assisting you.
Warmly,
Zachary Zouyed
Sales Support Representative
Subject: Assistance Required for Completing Institutional Subscription Application for Rebase
Date: Mon, 13 Nov 2023 14:12:34 +0000
From: Zhao, Yiyong <yz...@bwh.harvard.edu>
To: gi...@girinst.org <gi...@girinst.org>
CC: Dong, Xianjun <xdo...@bwh.harvard.edu>
Dear Rebase Support Team,
I hope this email finds you well.
This is Yiyong Zhao, a postdoctoral research fellow at Harvard University, and I am writing to seek your assistance with the approval process of an institutional subscription application for Harvard University.
Recently, I submitted a request through your website to have Rebase contact my institution's librarian regarding a subscription.
Your guidance in this matter would be greatly appreciated. I am looking forward to your positive response.
Thank you for your time and support.
Warm regards,
Yiyong Zhao
Yiyong(Rambo) Zhao, PhD
Genomics and Bioinformatics Hub
Harvard Medical School/Brigham and Women’s Hospital
TEL: +18573815442
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline .
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.