[genome] question - Table Browser restriction enzymes intersections

[Enrique Medina-Acosta]

Dear UCSC Genome Bioinformatics Group,

I wish to determine the coordinates at hg19 for a given methylation-sensitive restriction enzyme at genomic locations were public methylation studies (tracks) indicate that the said restriction site is consistently ummethylated, across several tissues. To accomplish that task, I am planning to use the intersection tool at the Table Browser. However, I could find the restriction enzyme table in the mapping and sequencing group (where it ought to be).

I appreciate your feedback.

Yours Enrique

Prof. Dr. Enrique Medina-Acosta, M.Sc., PhD.
MyCVLattes - CNPq
MyResearcherID (ISI Web of Knowledge)
MyORCID

Senior Associate Professor
Unit Coordinator - Molecular Identification and Diagnostics Unit - NUDIM
Laboratory of Biotechnology, Center for Biosciences and Biotechnology
Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF
Avenida Alberto Lamego 2000, Parque Califórnia, CEP 28013-602, Campos dos Goytacazes, RJ, Brazil.
Tel: +55 22 2726 6758 / +55 22 2739 7086

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[Robert Kuhn]

Hello, Enrique,

Thanks for being a sophisticated user of the Table Browser.  Unfortunately,
the Restriction Enzymes track is not available via the TB because the display
on the Browser graphic is generated in real time and there is no underlying
table.

However there is a workaround.  For any region, you can download the
coordinates of a single enz at a time (not more than one, however, sorry)
for a genomic interval by clicking on any one of the enzyme links in the

graphic.  E.g. for a region I happened to have open on hg19 chr6, I turned
on BamHI enzymes and clicked into it.  At the bottom of the upper section,

find:


Download BED of enzymes in this browser range:  all enzymes, just BamHI

and obtain, for BamHI:

chr6	31682874	31682880	BamHI	1000	+
chr6	31685872	31685878	BamHI	1000	+
chr6	31689308	31689314	BamHI	1000	+
chr6	31689511	31689517	BamHI	1000	+
chr6	31692885	31692891	BamHI	1000	+
chr6	31694866	31694872	BamHI	1000	+

You can make a custom track from these data and then pursue
the intersections you seek.

best wishes,

    --b0b kuhn
     ucsc genome bioinformatics group

--

[Enrique Medina-Acosta]

Great! I got it. That workaround will do it!

Many thanks.

Enrique

Prof. Dr. Enrique Medina-Acosta, M.Sc., PhD.
MyCVLattes - CNPq
MyResearcherID (ISI Web of Knowledge)
MyORCID

Senior Associate Professor
Unit Coordinator - Molecular Identification and Diagnostics Unit - NUDIM
Laboratory of Biotechnology, Center for Biosciences and Biotechnology
Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF
Avenida Alberto Lamego 2000, Parque Califórnia, CEP 28013-602, Campos dos Goytacazes, RJ, Brazil.
Tel: +55 22 2726 6758 / +55 22 2739 7086

========================================================================================
UENF - Serviços à comunidade oriundos de pesquisa translacional
=========================================================================================