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[Arabidopsis] rice gene model annotations from RAP-DB

Loraine, Ann via arab-gen%40net.bio.net (by Ann.Loraine from uncc.edu)
Thu Dec 19 08:28:42 EST 2013


Hello,

Recently some-one posted a question about the RAP-DB rice gene model annota=
tions.

In case this will be useful, we've added a new track for the RAP-DB gene mo=
dels to Integrated Genome Browser =96 http://bioviz.org/igb

The data are also available as a "BED-Detail" file from the IGBQuickLoad si=
te. (For information about BED-detail, see http://genome.ucsc.edu/FAQ/FAQfo=
rmat.html and to view a file listing of the rice IGBQuickLoad site go to ht=
tp://igbquickload.org/quickload/O_sativa_japonica_Oct_2011.)

When you visit the latest rice genome in IGB, two sets of gene models will =
load =96 including both the RAP-DB annotations (April 2013 releases) and al=
so the RGAP/MSU7 gene models.

Moving ahead we're aiming to create a non-redundant set of genes models and=
 functional annotations that will include both the RAP-DB and RGAP/MSU7 ann=
otations. The goal of this is to create a merged data set that will be usef=
ul for analysis of RNA-Seq, ChIP-Seq and microarray data sets. If you have =
thoughts on this or know of anyone who is also doing something similar, ple=
ase let us know.

All the best,

Ann

-------------------------------
Ann Loraine, Ph.D.
Associate Professor
Department of Bioinformatics and Genomics
University of North Carolina at Charlotte
North Carolina Research Campus
600 Laureate Way
Kannapolis, NC 28081
704-250-5750
aloraine from uncc.edu
http://www.transvar.org
http://www.bioviz.org
http://www.uncc.edu



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