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OriDB data for genome annotation

The files linked to below contain genome annotation data in BED and wiggle format. The coordinates used correspond to those used by the Yeast Genome Database in Oct 2003 and as used in the current S. cerevisiae release of the UCSC Genome Browser.

Origin locations:

OriDB Confirmed ARS set (based on current database):

Text file:
Link to UCSC Genome Browser Annotated with this data:
Link to paste into UCSC Genome Browser:
http://www.oridb.org/annotation_files/OriDB_confirmed_ARS.php

proARS from Wyrick et al. (2001):

Text file:
Link to UCSC Genome Browser Annotated with this data:
Link to paste into UCSC Genome Browser:
http://www.oridb.org/annotation_files/proARS.BED.txt

nimARS from Xu et al. (2006):

Text file:
Link to UCSC Genome Browser Annotated with this data:
Link to paste into UCSC Genome Browser:
http://www.oridb.org/annotation_files/Xu_calls.BED.txt

Replication timing data:

Note: in the UCSC genome browser curves (wiggle tracks) display with time running UP the y-axis (in contrast to OriDB and most chromosome replication publication which show time down the y-axis) this results in peaks corresponding to late replicating region and valleys correspond to early replicating regions (origins).

From Raghuraman et al. (2001):

Text file:
Link to UCSC Genome Browser Annotated with this data:
Link to paste into UCSC Genome Browser:
http://www.oridb.org/annotation_files/Raghu_timing.txt

From Yabuki et al. (2002):

Text file:
Link to UCSC Genome Browser Annotated with this data:
Link to paste into UCSC Genome Browser:
http://www.oridb.org/annotation_files/Yabuki_timing.txt

 

Chromatin immunoprecipitation (ChIP) of replication factors:

ORC ChIP from Xu et al. (2006):

Text file:
Link to UCSC Genome Browser Annotated with this data:
Link to paste into UCSC Genome Browser:
http://www.oridb.org/annotation_files/Xu_ORC.txt

Mcm2 ChIP from Xu et al. (2006):

Text file:
Link to UCSC Genome Browser Annotated with this data:
Link to paste into UCSC Genome Browser:
http://www.oridb.org/annotation_files/Xu_Mcm2.txt

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S. cerevisiae OriDB - v1.3.0.
Designed and maintained by Dr Conrad A. Nieduszynski & Dr Anne D. Donaldson