- How do I find out about a specific genome in
- How do I quickly find the genes I'm most
- Which genomes currently include diversity or
- Why do I have to register to access bulk
- What's up with version numbers? It
says I'm using Phytozome v10.1, but then the poplar version is 3.0 and
the soybean version is Wm82.a2.v1, etc. Help!
- I'm having real difficulties using Phytozome
in Internet Explorer. Any suggestions?
- I can't seem to scroll the organism images
on the home page, or JBrowse or.......
do I find out about a specific genome in Phytozome?
Each genome in Phytozome has an associated Organism Info page.
For example, the poplar page is here.
You can get to Organism Info pages either by selecting an organism from
the "Species" pulldown in the top menu, or, on the home page, by
double-clicking on the organism's photo in one of the three "Phytozome
quick start" panels. Theses pages have information on the assembly
and annotation of each genome, proper citation information, and a set of
quick links to get you to keyword and sequence searches, a JBrowse
genome browser, and bulk data download portals, all specific to that
do I quickly find the genes I'm most interested in?
From any of three "Phytozome quick start" panels on the home
page, you can select the organism you're interested in, by clicking on its
image (in the Flagship or Early Release panel), or start typing its name
in the "Target" box in the "Select from all..." panel), and then enter a
keyword or sequence fragment in the Query box, and click "GO". Your
keyword can be a gene identifier, a PFAM/GO/PANTHER or related id, a
descriptive term (e.g, kinesin, lignin, dessication), or gene symbol.
You'll be taken to a search
result or BLAST result list of related genes. You can work directly
with this set, or click "Revise query" on the side panel to refine or
alter your original search. "G" links take you to a gene detail
view, B links bring you to a view of the gene in its genomic
genomes currently include diversity or expression data?
Currently we have extensive diversity data for Poplar,
and smaller diversity data sets for Brachypodium,
On the gene pages for these species, an additional Variation
tab is present, showing SNPs and other variants in the neighborhood
of each each. RNA-Seq-based expression data is available for Poplar,
Soybean, and Phaseolus.
For these genomes, both expression and diversity data can also be viewed
in JBrowse, searched and downloaded
from PhytoMine, as well as in bulk from
the JGI Genome Portal. Note that expression and diversity data is not
available via our legacy BioMart instance.
do I have to register to access bulk data sets?
The Department of Energy and the Joint Genome Institute are committed to
providing free public access to the data and analyses generated here. In
order to justify the continued funding of public scientific resources such
as Phytozome, we need to document the large number of individuals, in
academia and industry, in the U.S. and abroad, who utilize our systems.
Registration information is obtained solely for the compilation of usage
statistics, and is not shared with any other U.S. Government or private
agency or individual.
What's up with version
numbers? It says I'm using Phytozome v10.1, but then the poplar
version is 3.0 and the soybean version is Wm82.a2.v1,
The Phytozome version number refers to a particular major release of the
Phytozome codebase, as well as a designated set of "released"
genomes. Minor release increments (e.g., 10.1, 10.2) usually involve
the addition of some new capability, data type, and/or several early
release genomes. X.x.x releases are typically bug fixes. This
versions have nothing to do with the versions of individual
genome assemblies and annotations. So, this conversation makes
sense: "I'm working with the v3 release of poplar. Where did
you get it?. From Phytozome v10." However, confusion
will follow if you tell people "I'm using v10.1 of poplar." The best
place to see all the version numbers of the genomes associted with a given
Phytozome release is on the Release
I'm having real difficulties
using Phytozome in Internet Explorer. Any suggestions?
Yes, stop using Internet Explorer. You should have a good
browsing experience with Firefox, Safari, or Chrome. If you must,
please make sure you're using IE 10 or later.
I can't seem to scroll the
organism images on the home page, or JBrowse or.......
If you are using a computer or laptop with a trackpad, scrollbars don't
always appear in scrollable sections until you actually put your cursor
over them and begin scrolling. So please give it a try. For
Mac OS X Lion or later users, there is an option in System Preferences->General->Show
scrollbars: Always , that will allow you to see scrollbars even when
you're not actively scrolling a section.