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[Arabidopsis] Updates at Araport

Town, Christopher D. via arab-gen%40net.bio.net (by cdtown from jcvi.org)
Fri Apr 3 15:22:02 EST 2015

ThaleMine and JBrowse have been updated at Araport. Some new features you may like are the incorporation of gene homologs in ThaleMine and a 1001 genomes track in JBrowse that allows you to see all the variants in and around your genes of interest and in which accessions they can be found.
Check it out!!


The Araport Team

ThaleMine was updated to version 1.5 on 03 April 2015. ThaleMine is available at https://apps.araport.org/thalemine/.

JBrowse was updated to version 1.11.6 on 03 April 2015. JBrowse is available at https://apps.araport.org/jbrowse/?data=arabidopsis.

Release Notes

Major Changes

 *   ThaleMine 1.5 incorporates homologs of Arabidopsis genes in many plant species computed by JGI using the InParanoid protocol and acquired from the Phytozome database [MINE-173].
 *   ThaleMine 1.5 incorporates mappings between Arabidopsis transcripts and their corresponding curated protein records from UniProt [MINE-445].
 *   JBrowse 1.11.6 incorporates a variant track from the 1001 Genomes project. Variant features are color coded using Ensembl's consequence diagram, and track data can be filtered by variant type [deletion, insertion, snv, etc.] and by consequence type [missense, intron_variant, frameshift variants, etc.]. Variation Features popup (available via a right-click menu) retrieves genotype, population and phenotype data using Ensembl's REST service. [MINE-709]

Minor Changes

 *   On ThaleMine gene or protein detail pages, in the Publications stripe, the source of the publication is now displayed as NCBI or UniProt, respectively [MINE-485].
 *   On ThaleMine gene or protein detail pages, in the Publications stripe, the records are now sorted in reverse chronological order [MINE-726].
 *   On a ThaleMine gene detail page, clicking on a GeneRIF now directs to a publication detail page with information about genes/proteins referenced in the publication [MINE-714].
 *   On a ThaleMine protein detail page, keywords from UniProt are now displayed in the summary at the top of the page [MINE-294].
 *   On ThaleMine detail pages, the external links on the right hand side are now ordered alphabetically and display a popup, on mouseover, with a brief description about the external database [MINE-443].
 *   On any ThaleMine page, clicking on the "Contact Us" link at the top (right) or the bottom (left) of the page now correctly focuses the user to a pre-filled contact form with details about errors, if any, encountered on the current page [MINE-454].

Chris Town
 J. Craig Venter Institute
9704 Medical Center Drive
Rockville, MD 20850
Office Phone: 301-795-7523
Fax: 301-795-7070
Home Phone: 301-990-0878
Cell Phone: 301-204-6300
SkypeID: chrisdtown

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