Walter, Mathias | 28 Mar 14:07 2015

GC-Content per frame, nucleotide composition

Hi!

Is it possible to display the GC-Content per frame (first, second and third position ) as an overlay graph like it is possible with Artemis (GC Frame Plot)?

Also, is there an easy way to show the di- and tri-nucleotide composition (triplet periodicity)? Or do I have to compute it myself and load it via bedgraph, for instance?

--
Kind regards,
Mathias
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Lishuang Shen | 27 Mar 05:12 2015
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gbrowse_create_account.pl a a bug with email setting?

We recently tried batch creation of accounts for a tutorial workshop of https://mseqdr.org

And we need to fix a potential bug (as below) to run.

We are running Gbrowse version 2.54

Lishuang

>>I found the error...

On the script /usr/local/bin/gbrowse_create_account.pl line 43 was:
'email-s'       => \$email,

instead of

'email=s'       => \$email,

I corrected it and now the command is working, takes a couple of seconds to create each account, I'll let you
know when all of them are created.

Daniel.

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Vaneet Lotay | 23 Mar 23:54 2015
Picon

Balloon click function

Hello,

 

I’m trying to add some links via tool tip for several tracks or as it’s called normally in the code the “balloon click” function.  These tracks are bigwig tracks.  For some reason simply trying to add that code to the respective configuration files causes the whole genome browser page not to be displayed, returns an “Internal Server error” page instead which I’ve seen before sometimes when some code cannot process properly from the .conf file.

 

Even when I add an empty function with no code like this it doesn’t work:

 

balloon click = sub{

}

 

This function and the same code that I’m trying to paste has worked for other types of tracks like gene model tracks, so I’m just wondering whether the Bigwig tracks simply don’t accept ‘balloon click’ as a function or not?  Is it not possible to add balloons or tool tips to bigwig tracks, if so how is it properly done?

 

Thanks,

 

Vaneet

 

Vaneet Lotay

Xenbase Bioinformatician

724 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

 

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display on GC Content and 6-frame translation

I have been installed GBrowse, and start configure it. But iI found some features can't display on my browse. but I can see all features of other's GBrowse.
I want to know what's wrong with my GBrowse, and where is my problem. 
yxx285223595-9Onoh4P/yGk@public.gmane.org
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Fernando Rodriguez | 21 Mar 02:47 2015

gbrowse is killing me

Hi,

It wasn't the first time I've installed gbrowser (previous attempts were good). But I just update (format) my desk computer and the installation of gbrowse is killing me.
So I've started with Biolinux 8 distribution; nothing came out of my browser. All paths seems clear, all prerequisites installed (apache working, etc etc). Well, there people complaining about Biolinux 8 distribution an gbrowse....lets re-format and install just ubuntu 14.04 LTS.....same troubles
...install apache, bioperl and download gbrowse2 (I think it is 2.55) from CPAN (also try with binary source)

The most I could do was getting a forbidden page on http://localhost/gb2/gbrowse/yeast.
And the frustrating thing is on the other side of my desk I have my laptop with gbrowse (2.42) well installed on ubuntu 12.04....looking and comparing folder by folder, file by file. Even with the tips I get at the Summer school in 2013, I am not able of doing it :(

Instead of losing time with details, could it be better to run it on a different os (fedora, centos)? Any other input would be appreciated. Thanks

--
Fernando Rodriguez, Ph.D.
Josephine Bay Paul Center for
Comparative Molecular Biology and Evolution
Marine Biological Laboratory
Woods Hole, MA 02543
Tel. (508) 289-7510
Fax: (508) 457-4727
frodriguez-vGvoHdrrOp8@public.gmane.org

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Hanny Elsadr | 13 Mar 21:05 2015
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Genetically Mapped Markers

Hello, 

My name is Hanny, I am contacting you from the University fo Guelph. 

In version 1.0 of the prunus persica GBrowse software I am able to see all of the genetically mapped markers
on the scaffold. I am unable to see this in version 2.1. How can I see the genetically mapped markers in
version 2.1?

Thank You

Hanny

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Michael Dondrup | 13 Mar 09:09 2015
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Picon

Exporting spliced mRNA or CDS sequence

Hi,

some of our users need to export the spliced mRNA sequence or CDS sequence only for designing primers. 
Is there a simple way or configuration option or plugin which allows to export spliced sequences?
I think that there should be an easy way, if I use the protein sequence dumper plugin, I get the identical 
protein sequence as predicted by maker for that gene model, so there should exist some correctly spliced
coding 
sequence in an intermediate step.

We are using GBrowse 2.54 with a chado backend and Bio::DB::DAS adapter. 

Michael Dondrup
Postdoctoral fellow
Sea Lice Research Centre/Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen, 
Norway

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Vladimir Gritsenko | 9 Mar 18:10 2015
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GBrowse 2.48 on Mac OS X Yosemite - tests fail

Hello all,

I realize that 2.48 is 3 years old, but the production environment I need to patch is 2.48, so here I am.

The full error log is here: http://pastebin.com/sbFKycHi , but the gist of is that there are a lot of error messages that look like this:

http://localhost:57649; search failed: 500 Can't connect to localhost:57649 (Connection refused) at /Users/bermanlab/dev/GBrowse/t/../lib/Bio/Graphics/Browser2/RegionSearch.pm line 563.

Thanks!
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Rayapadi Swetha | 4 Mar 12:59 2015
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Fwd: Need a help


Dear Sir,

Tons of thanks. I followed your suggestion, option 2. Now it works well. You helped me a lot in GBrowse (Starting from installation to till now). Thank you so much. I used GBrowse in two databases and both are published. One in Genomics and other in Computers in Biology and Medicine. This publication is not possible without your guidance.

Thank you.

Yours sincerely,
Swetha R G,
Research Associate,
School of BioSciences and Technology,
VIT University,
India.

On Thu, Nov 27, 2014 at 9:27 AM, Rayapadi Swetha <swetha.rayapadi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Dear Sir,

Thank you so much for your quick reply. Let me work according to your suggestion and If I stuck at any point, Please help me.

Yours sincerely,
Swetha R G.

On Wed, Nov 26, 2014 at 9:53 PM, Scott Cain <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org> wrote:
Hi Swetha,

The only way I can think of to do that is with separate configuration files for GBrowse unfortunately.  The "data source" drop down was originally conceived of to allow selecting different "species", but that concept doesn't map very well to strains of a virus.  There are two approaches I could see using:

1. Revamp the way you're using GBrowse data sources altogether, so that each data source represents one type of virus, so in the drop down you'd have two entries, one for H. influenzae and one for the other virus.  Each strain would then be analogous a chromosome. One advantage to this approach is that when/if you have hundreds of strains of a virus the drop down will still be useable (that is, a drop down menu with a more than 20-30 entries is very unwieldy).  Users would be able to use the search box to find strains they are interested in.  A potential downside is that searching for a particular gene would yield results for that gene in every strain.

2. Create separate gbrowse2 config directories for each virus.  Then you need to edit gbrowse2.conf file that lives in the apache configuration; where that is varies depending on your OS; on Ubuntu 12.04 it's in /etc/apache2/conf.d/.  You'll need separate cgi-bin directories too, for example you could have /usr/lib/cgi-bin/Higb2/ for influenzae and /usr/lib/cgi-bin/Segb2 for the Something else virus :-)  In the apache gbrowse.conf file you need separate entries for the different cgi-bin directores that have different "SetEnv GBROWSE_CONF" entries to point at the separate gbrowse config directories.

Obviously, it's up to you to decide which is better; there will be work either way.  I suggest that if you choose the second path that you make very incremental changes and test that GBrowse still works all along the way, because there are several moving parts that could break GBrowse and with the changes required, it might be difficult to sort out what happened if something goes wrong.

Scott


On Wed, Nov 26, 2014 at 10:13 AM, Rayapadi Swetha <swetha.rayapadi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Respected Sir,

We have developed a database for Haemophilus influenzae and we used Gbrowse to visualize their annotation. Now, we are developing the database for other organism and we need to use the Gbrowse. We are going to host the second database in the same server where GBrowse is already installed. But, I have a doubt. The dropdown menu for the second database should be changed in GBrowse. How is it possible?

For example:

In Haemophilus influenzae database, we have included 10 different strains of H. influenzae. I have attached the screenshot for your reference.

In second database, I need to include 25 strains of other organism.

Query: these 25 strains should be in dropdown menu instead of those 10 strains. And, When the user access H. influenzae database, 10 strains should be there and when the user access second database, 25 strains should be there. How is it possible?

Waiting for your reply.

Yours sincerely,
Swetha R G.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



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Scott Cain | 4 Mar 15:14 2015
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Re: Need a help

Hi Swetha,

Please always ask questions on the mailing list (cc'ed here).

If you are using fastcgi, you may need to restart apache to recognize the change you made in your config file.  The other possibility is that you didn't really edit the config file that GBrowse is using (believe me, I've done that many times, where I edit a copy of the config file and can't understand why it isn't having any effect).

Scott


On Wed, Mar 4, 2015 at 6:58 AM, Rayapadi Swetha <swetha.rayapadi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Dear Sir,

I have a doubt in Gbrowse. Can you please help me sir?

Herewith, I have attached the conf file.


It works well in Browser. In file, suppose, If I change initial landmark = NC_022659.1:1..10000 to initial landmark = NC_022659.1:20639..15623, the browser displays the old landmark itself (i.e 1..10000). I know its because of some cache problem. If I delete the browser history, then the browser displays the new landmark. Can you please solve this issue?

Yours sincerely,
Swetha R G,
Senior Research Fellow (ICMR),
VIT University,
Vellore,
India.








On Thu, Nov 27, 2014 at 8:21 PM, Rayapadi Swetha <swetha.rayapadi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Dear Sir,

Tons of thanks. I followed your suggestion, option 2. Now it works well. You helped me a lot in GBrowse (Starting from installation to till now). Thank you so much. I used GBrowse in two databases and both are published. One in Genomics and other in Computers in Biology and Medicine. This publication is not possible without your guidance.

Thank you.

Yours sincerely,
Swetha R G,
Research Associate,
School of BioSciences and Technology,
VIT University,
India.

On Thu, Nov 27, 2014 at 9:27 AM, Rayapadi Swetha <swetha.rayapadi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Dear Sir,

Thank you so much for your quick reply. Let me work according to your suggestion and If I stuck at any point, Please help me.

Yours sincerely,
Swetha R G.

On Wed, Nov 26, 2014 at 9:53 PM, Scott Cain <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org> wrote:
Hi Swetha,

The only way I can think of to do that is with separate configuration files for GBrowse unfortunately.  The "data source" drop down was originally conceived of to allow selecting different "species", but that concept doesn't map very well to strains of a virus.  There are two approaches I could see using:

1. Revamp the way you're using GBrowse data sources altogether, so that each data source represents one type of virus, so in the drop down you'd have two entries, one for H. influenzae and one for the other virus.  Each strain would then be analogous a chromosome. One advantage to this approach is that when/if you have hundreds of strains of a virus the drop down will still be useable (that is, a drop down menu with a more than 20-30 entries is very unwieldy).  Users would be able to use the search box to find strains they are interested in.  A potential downside is that searching for a particular gene would yield results for that gene in every strain.

2. Create separate gbrowse2 config directories for each virus.  Then you need to edit gbrowse2.conf file that lives in the apache configuration; where that is varies depending on your OS; on Ubuntu 12.04 it's in /etc/apache2/conf.d/.  You'll need separate cgi-bin directories too, for example you could have /usr/lib/cgi-bin/Higb2/ for influenzae and /usr/lib/cgi-bin/Segb2 for the Something else virus :-)  In the apache gbrowse.conf file you need separate entries for the different cgi-bin directores that have different "SetEnv GBROWSE_CONF" entries to point at the separate gbrowse config directories.

Obviously, it's up to you to decide which is better; there will be work either way.  I suggest that if you choose the second path that you make very incremental changes and test that GBrowse still works all along the way, because there are several moving parts that could break GBrowse and with the changes required, it might be difficult to sort out what happened if something goes wrong.

Scott


On Wed, Nov 26, 2014 at 10:13 AM, Rayapadi Swetha <swetha.rayapadi <at> gmail.com> wrote:
Respected Sir,

We have developed a database for Haemophilus influenzae and we used Gbrowse to visualize their annotation. Now, we are developing the database for other organism and we need to use the Gbrowse. We are going to host the second database in the same server where GBrowse is already installed. But, I have a doubt. The dropdown menu for the second database should be changed in GBrowse. How is it possible?

For example:

In Haemophilus influenzae database, we have included 10 different strains of H. influenzae. I have attached the screenshot for your reference.

In second database, I need to include 25 strains of other organism.

Query: these 25 strains should be in dropdown menu instead of those 10 strains. And, When the user access H. influenzae database, 10 strains should be there and when the user access second database, 25 strains should be there. How is it possible?

Waiting for your reply.

Yours sincerely,
Swetha R G.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research






--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Sam Hokin | 4 Mar 05:34 2015

Search on load_id attribute (Ensembl genomes)?

Hi, folks, just joined the list after spending a lot of time with GBrowse the past few months. My question: Is
there any way to get 
search to search on the load_id attribute?

Annotated genes that I get from the Ensembl plant database (I'm working with the maize AGPv3 genome, aka
B73_RefGen_v3) do not have 
a Name attribute in the GFF3 file. Here's a typical line from Zea_mays.AGPv3.24.gff3 (swapping spaces for tabs):

10 ensembl gene 28054052 28054433 . + .
ID=gene:GRMZM5G846142;assembly_name=AGPv3;biotype=protein_coding;description=Uncharacterized 
protein  [Source:UniProtKB/TrEMBL%3BAcc:K7TYI5];logic_name=genebuilder;version=1

A lot of wonderful info there in the attributes, but no Name is provided. This gets loaded into my database
(using 
bp_seqfeature_load.pl) with load_id=gene:GRMZM5G846142 and no Name. If one searches for
"GRMZM5G846142" or "gene:GRMZM5G846142" in 
the browser, one gets Not Found. (Oddly, Ensembl does provide a Name attribute for exons; but not genes,
transcripts or CDS, at 
least in the current version - and by the way, the color-coded GFF3 parent-child relationship display
works wonderfully with those!)

Yes, I can futz with the GFF file, or run a SQL script to insert a record in name for all load_id records in
attributes that don't 
have one in name, and all sorts of things, but I thought maybe there's a way to avoid that in a conf file.
Ensembl is a pretty big 
source of genome data, so I'd think this would come up a lot.

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