Re: [genome] Query

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Jonathan Casper

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Mar 24, 2015, 11:53:41 PM3/24/15
to Talyan, Sweta, genome...@soe.ucsc.edu, gen...@soe.ucsc.edu

Hello Sweta,

Thank you for your question about locating a reference for the 100-way multiple alignment and conservation track on the human hg19 genome assembly. We provide a citation page at http://genome.ucsc.edu/cite.html that contains commonly used references for our site and displayed data. The 100-way track that you refer to is actually included in our most recent update of the UCSC Genome Browser database, found on our publications page; a citation follows.

Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, Karolchik D, Learned K, Lee BT, Li CH, Miga KH, Nguyen N, Paten B, Raney BJ, Smit AF, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ. The UCSC Genome Browser database: 2015 update. Nucleic Acids Res. 2015 Jan 28;43(Database issue):D670-81. doi: 10.1093/nar/gku1177. Epub 2014 Nov 26. PMID: 25428374

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group


On Tue, Mar 24, 2015 at 1:00 PM, Talyan, Sweta <S.Ta...@imb-mainz.de> wrote:

Dear,


I have used the following UCSC track of 100 vertebrates Conserved Elements, which give information about the conserved elements across 100 verterbrates.

I wish to refer this study in the manuscript for publication. But I am unable to find suitable reference.

Could you please help me with this.


I tried to explore the following webpage but unable to get the reference

http://genome.ucsc.edu/cgi-bin/hgc?hgsid=419944183_SK2J4Ac1auCJBa1gXRv9Om61AGWa&c=chr3&o=33040638&t=33040655&g=phastConsElements100way&i=lod%3D78



Sweta Talyan
Computational Biology & Data Mining
Johannes Gutenberg University Mainz
Institute of Molecular Biology
Ackermannweg 4, 55128 Mainz Germany

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Talyan, Sweta

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Mar 27, 2015, 11:30:03 AM3/27/15
to genome...@soe.ucsc.edu, gen...@soe.ucsc.edu

Can you please suggest a paper where the term "100 vertebrates conserved elements" is nicely explained ?


Regards
Sweta Talyan
From: Talyan, Sweta
Sent: Wednesday, March 25, 2015 12:44 PM
To: Jonathan Casper; genome...@soe.ucsc.edu; gen...@soe.ucsc.edu
Subject: Re: [genome] Query
 

Hello Jonathan,


I have looked at the reference which you mentioned but this paper doesn’t describe the method or the strategy used to retrieve these conserved element from 100 vertebrates (a combination of phylop-HMM and Phast-cons).


I would be highly obliged if you point me to the original paper or the method which describes the how 100 vertebrates conserved elements was retrieved by the combination of Phylo-HMMs, phastCons, and phyloP.


Thanking you for your prompt response and the above mentioned reference.



Sweta Talyan
Computational Biology & Data Mining
Johannes Gutenberg University Mainz
Institute of Molecular Biology
Ackermannweg 4, 55128 Mainz Germany
From: Jonathan Casper <jca...@soe.ucsc.edu>
Sent: Wednesday, March 25, 2015 4:53 AM
To: Talyan, Sweta
Cc: genome...@soe.ucsc.edu; gen...@soe.ucsc.edu
Subject: Re: [genome] Query
 
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