[Gmod-ajax] Displaying protein-sequence alignments

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

[Gmod-ajax] Displaying protein-sequence alignments

Eric Rasche-3
Howdy all,

I've been doing a lot with displaying of blast results in JBrowse, and was wondering if anyone had solutions to showing the actual alignment of the blast hit to the parent sequence in JBrowse. Ideally the alignment would be visible when viewing a feature, but I just haven't had any bright ideas. Should I write a plugin that'll produce a popup? Does something else that does this exist? I saw some recent threads on getting the protein sequence of a feature, so I know that much is possible. Do I need to embed the pairwise alignment in a giant Note="" in my GFF3?

Ideally there would be a way to view a pairwise alignment (example below) from the right click menu of one of the blast hit features.

Query 61 ALHALVAPPACAGSPARHAQPEPQQ 85
         ALHALVAPPACAG PARHAQPEPQQ

Sbjct 61 ALHALVAPPACAGDPARHAQPEPQQ 85
 
Just for kicks, here's the blast in JBrowse stuff which shows gapped alignments with opacity coded to e-values.




-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048
[hidden email]

------------------------------------------------------------------------------

_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: Displaying protein-sequence alignments

Saari, Travis

Hi Eric,

 

I’m by no means an expert, but I’ve got a simple solution if you’re willing to re-run the blasts again. It will display all of your blast results as HTML, almost like the web version. This should be really easy to implement. I tested it out briefly and it works for me. Others should chip in to let you know of any other solutions.

 

Re-run the blast, and set the output as html with the -html flag. Run each query separately and name them according to how your features are named in your track. You probably want to set the max_target_seqs to a reasonable number so that you don’t have to scroll through a ton of stuff (Although the awesome thing is that each hit is linked in the initial list, and you can jump to the one you’re interested in).

 

Put all these html files in a place accessible to the browser such as your data folder.

 

Modify the menuTemplate in that track to include a new entry :

“menuTemplate” [

                {},

                {},

                {

                “label” : “View BLAST as HTML”,

                “iconClass” : “dijitIconBookmark”,

                “url” : “data/sub-folder/{name}.html”  // I actually had to use {id}, but I think this depends on your tags

                }

   ]

 

Hope this helps!

 

 

Travis Saari

Student Services Contractor at

US-EPA

Mid-Continent Ecology Division

218. 529.5178

 

 

 

From: Eric Rasche [mailto:[hidden email]]
Sent: Wednesday, December 23, 2015 11:21 AM
To: [hidden email]
Subject: [Gmod-ajax] Displaying protein-sequence alignments

 

Howdy all,

I've been doing a lot with displaying of blast results in JBrowse, and was wondering if anyone had solutions to showing the actual alignment of the blast hit to the parent sequence in JBrowse. Ideally the alignment would be visible when viewing a feature, but I just haven't had any bright ideas. Should I write a plugin that'll produce a popup? Does something else that does this exist? I saw some recent threads on getting the protein sequence of a feature, so I know that much is possible. Do I need to embed the pairwise alignment in a giant Note="" in my GFF3?

Ideally there would be a way to view a pairwise alignment (example below) from the right click menu of one of the blast hit features.

Query 61 ALHALVAPPACAGSPARHAQPEPQQ 85
         ALHALVAPPACAG PARHAQPEPQQ
Sbjct 61 ALHALVAPPACAGDPARHAQPEPQQ 85

 
Just for kicks, here's the blast in JBrowse stuff which shows gapped alignments with opacity coded to e-values.





-- 
Eric Rasche
Programmer II
 
Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048
[hidden email]

------------------------------------------------------------------------------

_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: Displaying protein-sequence alignments

Eric Rasche-3
Hi Travis,

On 12/23/2015 01:12 PM, Saari, Travis wrote:

Hi Eric,

 

I’m by no means an expert, but I’ve got a simple solution if you’re willing to re-run the blasts again. It will display all of your blast results as HTML, almost like the web version. This should be really easy to implement. I tested it out briefly and it works for me. Others should chip in to let you know of any other solutions.

 

Re-run the blast, and set the output as html with the -html flag. Run each query separately and name them according to how your features are named in your track. You probably want to set the max_target_seqs to a reasonable number so that you don’t have to scroll through a ton of stuff (Although the awesome thing is that each hit is linked in the initial list, and you can jump to the one you’re interested in).

Huh! That's a really ingenious solution, I never would've thought to just display the html pages, and that will take care of both nucleotide and protein alignments.

 

Put all these html files in a place accessible to the browser such as your data folder.

 

Modify the menuTemplate in that track to include a new entry :

“menuTemplate” [

                {},

                {},

                {

                “label” : “View BLAST as HTML”,

                “iconClass” : “dijitIconBookmark”,

                “url” : “data/sub-folder/{name}.html”  // I actually had to use {id}, but I think this depends on your tags

                }

   ]

 

Hope this helps!

Thanks, I'll definitely try this out to see how it works for us. I wonder if there aren't other more tightly integrated solutions (e.g. displaying the alignment on top of the CanvasFeature or something, given that we use Apollo, JBrowse, Chado, etc), but this will definitely be a workable stopgap!

 

 

Travis Saari

Student Services Contractor at

US-EPA

Mid-Continent Ecology Division

218. 529.5178

 

 

 

From: Eric Rasche [[hidden email]]
Sent: Wednesday, December 23, 2015 11:21 AM
To: [hidden email]
Subject: [Gmod-ajax] Displaying protein-sequence alignments

 

Howdy all,

I've been doing a lot with displaying of blast results in JBrowse, and was wondering if anyone had solutions to showing the actual alignment of the blast hit to the parent sequence in JBrowse. Ideally the alignment would be visible when viewing a feature, but I just haven't had any bright ideas. Should I write a plugin that'll produce a popup? Does something else that does this exist? I saw some recent threads on getting the protein sequence of a feature, so I know that much is possible. Do I need to embed the pairwise alignment in a giant Note="" in my GFF3?

Ideally there would be a way to view a pairwise alignment (example below) from the right click menu of one of the blast hit features.

Query 61 ALHALVAPPACAGSPARHAQPEPQQ 85
         ALHALVAPPACAG PARHAQPEPQQ
Sbjct 61 ALHALVAPPACAGDPARHAQPEPQQ 85

 
Just for kicks, here's the blast in JBrowse stuff which shows gapped alignments with opacity coded to e-values.





-- 
Eric Rasche
Programmer II
 
Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048
[hidden email]
Cheers,
Eric

-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048
[hidden email]

------------------------------------------------------------------------------

_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: Displaying protein-sequence alignments

Suzanna Lewis-3
It might be while, but the hope is that we'll incorporate the MSA widget from BioJS

http://biojs.io/d/msa

I had (some small) influence in requirements when it was being implemented, so I'm hoping it will be relatively straightforward to take on. (volunteers always welcome!)

-S
 

On Mon, Dec 28, 2015 at 8:56 AM, Eric Rasche <[hidden email]> wrote:
Hi Travis,

On 12/23/2015 01:12 PM, Saari, Travis wrote:

Hi Eric,

 

I’m by no means an expert, but I’ve got a simple solution if you’re willing to re-run the blasts again. It will display all of your blast results as HTML, almost like the web version. This should be really easy to implement. I tested it out briefly and it works for me. Others should chip in to let you know of any other solutions.

 

Re-run the blast, and set the output as html with the -html flag. Run each query separately and name them according to how your features are named in your track. You probably want to set the max_target_seqs to a reasonable number so that you don’t have to scroll through a ton of stuff (Although the awesome thing is that each hit is linked in the initial list, and you can jump to the one you’re interested in).

Huh! That's a really ingenious solution, I never would've thought to just display the html pages, and that will take care of both nucleotide and protein alignments.

 

Put all these html files in a place accessible to the browser such as your data folder.

 

Modify the menuTemplate in that track to include a new entry :

“menuTemplate” [

                {},

                {},

                {

                “label” : “View BLAST as HTML”,

                “iconClass” : “dijitIconBookmark”,

                “url” : “data/sub-folder/{name}.html”  // I actually had to use {id}, but I think this depends on your tags

                }

   ]

 

Hope this helps!

Thanks, I'll definitely try this out to see how it works for us. I wonder if there aren't other more tightly integrated solutions (e.g. displaying the alignment on top of the CanvasFeature or something, given that we use Apollo, JBrowse, Chado, etc), but this will definitely be a workable stopgap!

 

 

Travis Saari

Student Services Contractor at

US-EPA

Mid-Continent Ecology Division

218. 529.5178

 

 

 

From: Eric Rasche [[hidden email]]
Sent: Wednesday, December 23, 2015 11:21 AM
To: [hidden email]
Subject: [Gmod-ajax] Displaying protein-sequence alignments

 

Howdy all,

I've been doing a lot with displaying of blast results in JBrowse, and was wondering if anyone had solutions to showing the actual alignment of the blast hit to the parent sequence in JBrowse. Ideally the alignment would be visible when viewing a feature, but I just haven't had any bright ideas. Should I write a plugin that'll produce a popup? Does something else that does this exist? I saw some recent threads on getting the protein sequence of a feature, so I know that much is possible. Do I need to embed the pairwise alignment in a giant Note="" in my GFF3?

Ideally there would be a way to view a pairwise alignment (example below) from the right click menu of one of the blast hit features.

Query 61 ALHALVAPPACAGSPARHAQPEPQQ 85
         ALHALVAPPACAG PARHAQPEPQQ
Sbjct 61 ALHALVAPPACAGDPARHAQPEPQQ 85

 
Just for kicks, here's the blast in JBrowse stuff which shows gapped alignments with opacity coded to e-values.





-- 
Eric Rasche
Programmer II
 
Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
<a href="tel:404-692-2048" value="+14046922048" target="_blank">404-692-2048
[hidden email]
Cheers,
Eric

-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
<a href="tel:404-692-2048" value="+14046922048" target="_blank">404-692-2048
[hidden email]

------------------------------------------------------------------------------

_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------

_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax