GenBank accessions disappearing from the genome browser

Tong Hao

unread,

Apr 30, 2015, 4:14:14 PM4/30/15

to gen...@soe.ucsc.edu, Hill, David E., Yun_...@dfci.harvard.edu

Hi there,

It came to our attention that more than 10,000 GenBank accessions from following paper disappeared.

AUTHORS   Yang,X., Boehm,J.S., Yang,X., Salehi-Ashtiani,K., Hao,T., Shen,Y.,
            Lubonja,R., Thomas,S.R., Alkan,O., Bhimdi,T., Green,T.M.,
            Johannessen,C.M., Silver,S.J., Nguyen,C., Murray,R.R.,
            Hieronymus,H., Balcha,D., Fan,C., Lin,C., Ghamsari,L., Vidal,M.,
            Hahn,W.C., Hill,D.E. and Root,D.E.
TITLE     A public genome-scale lentiviral expression library of human ORFs
JOURNAL   Nat. Methods 8 (8), 659-661 (2011)
PUBMED   21706014

They were visible on the "Human mRNA from GenBank" track roughly a month ago after we updated these records to include "Homo sapiens" as their source.

A couple of examples for you to look at:

http://www.ncbi.nlm.nih.gov/nuccore/KJ892028
http://www.ncbi.nlm.nih.gov/nuccore/KJ899678

Thanks in advance for your kindly assistance. Please feel free to contact us should you need more info.

Best,

Tong

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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Matthew Speir

unread,

May 1, 2015, 1:38:58 PM5/1/15

to Tong Hao, gen...@soe.ucsc.edu, Hill, David E., Yun_...@dfci.harvard.edu

Hi Tong,

Thank you for your report about these sequences that have gone missing from the "Human mRNAs from GenBank" track. These sequences were dropped due to some problems with the pipeline we use to generate this mRNA track and other, similar GenBank tracks. We hope to have these issues resolved soon, which should restore these missing accessions to the "Human mRNAs from GenBank" track.

I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

--

Tong Hao

unread,

May 1, 2015, 2:12:45 PM5/1/15

to Matthew Speir, gen...@soe.ucsc.edu, Hill, David E., Yun_...@dfci.harvard.edu

Dear Matthew,

Thank you for your quick reply and clear explanation. We will be truly grateful if you could keep us posted.

Best,

Tong

Reply all

Reply to author

Forward