[Genome] Gene density and centromeres

[Marius...@stud.unibas.ch]

Hello everyone,

I'd like to create a heat map (gene densities). ENSEMBL offers a graph
for gene densities (they distinguish between "known" and "novel"
genes). However, I contacted the people from ENSEMBL, but apparently
these gene density data cannot be downloaded (neither the graph):

http://www.ensembl.org/Tetraodon_nigroviridis/Location/Chromosome?r=1:783604-1032531

Is there a way to get such a graph or all the info to plot such a
graph oneself from UCSC? Where can I get it?

And: How reliable/trustworthy are these data? As I've seen in ENSEMBL,
most genes of the ""non-model"" organisms (i.e. Medaka) are
categorized as "novel genes". Are these genes predicted by homology
when compared to other genomes?



Also, I'd like to know, how I can find the exact position of the
centromeres of the ""non-model"" organism genomes (i.e. stickleback)?

Thank you a lot for your help,

Marius




----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.

[Brooke Rhead]

Hi Marius,

Have you seen the Genome Graphs tool?
http://genome.ucsc.edu/cgi-bin/hgGenome
(You can also get to it by hitting the "Home" link and then "Genome
Graphs" on the left-hand menu.)

To create a density graph for any existing track, hit the "import"
button, select the track from the drop-down menus, optionally give it a
name, then hit "submit". Once the track has been loaded, you have to
select it from the "graph" drop-down menu to see it. For more details,
see the User's Guide:
http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html

> And: How reliable/trustworthy are these data?

That depends on which track you are viewing. To read about the data
sources and methods used to create any of the tracks in the Genome
Browser, go to the main Browser page
(http://genome.ucsc.edu/cgi-bin/hgTracks) and either click on the blue
track name above the drop-down menus, or click on the gray button
directly to the left of a track that is already displayed.

> Also, I'd like to know, how I can find the exact position of the
> centromeres of the ""non-model"" organism genomes (i.e. stickleback)?

This information is not available for all organisms. If it is
available, it will be described in the "Gap" track.

I hope this information is helpful. If you have further questions,
please feel free to contact us again at gen...@soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

> _______________________________________________
> Genome maillist - Gen...@soe.ucsc.edu
> https://lists.soe.ucsc.edu/mailman/listinfo/genome

[Brooke Rhead]

Hi Marius,

I forgot to mention that the density data generated by importing a track
into Genome Graphs are available in the Table Browser
(http://genome.ucsc.edu/cgi-bin/hgTables) via the "group: Custom Tracks"
menu. You can download the data by selecting "region: genome" and
entering a name for the file in the "output file" box.

--
Brooke Rhead
UCSC Genome Bioinformatics Group