Set up GBrowse to compare the genes of n number of isolates

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

Set up GBrowse to compare the genes of n number of isolates

Wiese, Matthew B.

GBrowse Team,


I'm setting up a GBrowse system for my lab's particular data on fungi.


The researchers would like to use GBrowse to compare the gene differences between two or more isolates.


I've looked through the wiki and have tried web searches but nothing has come up.


Is it possible to modify GBrowse to view multiple genomes and compare their differences in genes?



Thanks,

Matt Wiese


------------------------------------------------------------------------------
Monitor 25 network devices or servers for free with OpManager!
OpManager is web-based network management software that monitors
network devices and physical & virtual servers, alerts via email & sms
for fault. Monitor 25 devices for free with no restriction. Download now
http://ad.doubleclick.net/ddm/clk/292181274;119417398;o
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Set up GBrowse to compare the genes of n number of isolates

Alexey Morozov
I don't think you can easily add real support for multiple genomes in gbrowse. What you can do is emulate it. Add a separate track with data about presence of a given gene in other genomes and add hyperlinks to those in that track, like this:

              |||||||||||||||||||||||||||||||||||||||||||||||||||||    Gene track
Strain 2  |||||<link to strain2>||||||||||||||||||||    Hyperlink and some data about genes' identity or whatever
Strain 3                                                       No link here because strain 3 doesn't contain this gene
Strain 4 |||||<link to strain4>|||||||||||||||||||||    Like Strain 2

There are no reasons not to make these tracks look like "Real" gene track. But keep in mind that you lose any possible rearrangements data (there may be a separate track for contiguous segments, too!) and lengths of blocks for other strains will be bound to Strain 1 gene length.

2015-06-25 13:29 GMT+08:00 Wiese, Matthew B. <[hidden email]>:

GBrowse Team,


I'm setting up a GBrowse system for my lab's particular data on fungi.


The researchers would like to use GBrowse to compare the gene differences between two or more isolates.


I've looked through the wiki and have tried web searches but nothing has come up.


Is it possible to modify GBrowse to view multiple genomes and compare their differences in genes?



Thanks,

Matt Wiese


------------------------------------------------------------------------------
Monitor 25 network devices or servers for free with OpManager!
OpManager is web-based network management software that monitors
network devices and physical & virtual servers, alerts via email & sms
for fault. Monitor 25 devices for free with no restriction. Download now
http://ad.doubleclick.net/ddm/clk/292181274;119417398;o
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.

------------------------------------------------------------------------------
Monitor 25 network devices or servers for free with OpManager!
OpManager is web-based network management software that monitors
network devices and physical & virtual servers, alerts via email & sms
for fault. Monitor 25 devices for free with no restriction. Download now
http://ad.doubleclick.net/ddm/clk/292181274;119417398;o
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Set up GBrowse to compare the genes of n number of isolates

Michael Dondrup-3
Hi,

there is also GBrowse syn http://gmod.org/wiki/GBrowse_syn 

Best
Michael

On Jun 25, 2015, at 10:00 AM, Alexey Morozov wrote:

> I don't think you can easily add real support for multiple genomes in gbrowse. What you can do is emulate it. Add a separate track with data about presence of a given gene in other genomes and add hyperlinks to those in that track, like this:
>
>               |||||||||||||||||||||||||||||||||||||||||||||||||||||    Gene track
> Strain 2  |||||<link to strain2>||||||||||||||||||||    Hyperlink and some data about genes' identity or whatever
> Strain 3                                                       No link here because strain 3 doesn't contain this gene
> Strain 4 |||||<link to strain4>|||||||||||||||||||||    Like Strain 2
>
> There are no reasons not to make these tracks look like "Real" gene track. But keep in mind that you lose any possible rearrangements data (there may be a separate track for contiguous segments, too!) and lengths of blocks for other strains will be bound to Strain 1 gene length.
>
> 2015-06-25 13:29 GMT+08:00 Wiese, Matthew B. <[hidden email]>:
> GBrowse Team,
>
> I'm setting up a GBrowse system for my lab's particular data on fungi.
>
> The researchers would like to use GBrowse to compare the gene differences between two or more isolates.
>
> I've looked through the wiki and have tried web searches but nothing has come up.
>
> Is it possible to modify GBrowse to view multiple genomes and compare their differences in genes?
>
>
> Thanks,
> Matt Wiese
>
> ------------------------------------------------------------------------------
> Monitor 25 network devices or servers for free with OpManager!
> OpManager is web-based network management software that monitors
> network devices and physical & virtual servers, alerts via email & sms
> for fault. Monitor 25 devices for free with no restriction. Download now
> http://ad.doubleclick.net/ddm/clk/292181274;119417398;o
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> Alexey Morozov,
> LIN SB RAS, bioinformatics group.
> Irkutsk, Russia.
> ------------------------------------------------------------------------------
> Monitor 25 network devices or servers for free with OpManager!
> OpManager is web-based network management software that monitors
> network devices and physical & virtual servers, alerts via email & sms
> for fault. Monitor 25 devices for free with no restriction. Download now
> http://ad.doubleclick.net/ddm/clk/292181274;119417398;o_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


------------------------------------------------------------------------------
Monitor 25 network devices or servers for free with OpManager!
OpManager is web-based network management software that monitors
network devices and physical & virtual servers, alerts via email & sms
for fault. Monitor 25 devices for free with no restriction. Download now
http://ad.doubleclick.net/ddm/clk/292181274;119417398;o
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse