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RoshanShrestha123

opened on Oct 20, 2021

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Hello,

I am software developer (new to biojava) currently using the Biojava API [biojava-core - 4.0.0 , alignment -1.9.3] for an application.

We are trying to accomplish Alignment render of the Query and the target
on Blast search like the image below. We are using the SmithWaterman algorithm for local Alignment. Now we are looking for a different way to visualize exactly where the sequence was aligned in our frontend application (we are using biojava in our backend side), like the following.

AAGAA
||| |
AAGGA

I found SimpleAlignment to render query and target alignment using TranslatedSequencePanel. but SimpleAlignment does not handle different length sequences and does not contain any gap-editing concepts. Upon further research I also came across formatOut which return string with the format we were looking for. But formatOut is only available in biojava-legacy. Is there any way i can get the result like this one?

Thanks!

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1. willishf commented on Oct 20, 2021

   

   willishf

   on Oct 20, 2021 via email

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   Not sure of the current status of the RichSequenceViewer that I put together many many years ago and probably in BioJava legacy at this point but should be what you are looking for. https://biojava.org/wiki/BioJava:CookBook:Interfaces:ProteinPeptideFeatures found at https://biojava.org/wiki/BioJava:CookBookLegacy as well as https://biojava.org/wiki/BioJava:CookBook:Interfaces:Alignments You can do just about anything related to the work for displaying a sequence, have it auto wrap when resize and then draw features etc that are graphic elements etc. If you have Java GUI background you should be able to

   …

   On Wed, Oct 20, 2021 at 3:57 AM Roshan Shrestha ***@***.***> wrote: Hello, I am software developer (new to biojava) currently using the Biojava API [biojava-core - 4.0.0 , alignment -1.9.3] for an application. We are trying to accomplish Alignment render of the Query and the target on Blast search like the image below. We are using the SmithWaterman algorithm for local Alignment. Now we are looking for a different way to visualize exactly where the sequence was aligned in our frontend application (we are using biojava in our backend side), like the following. AAGAA ||| | AAGGA I found SimpleAlignment to render query and target alignment using TranslatedSequencePanel. but SimpleAlignment does not handle different length sequences and does not contain any gap-editing concepts. Upon further research I also came across formatOut which return string with the format we were looking for. But formatOut is only available in biojava-legacy. Is there any way i can get the result like this one? [image: image] <https://user-images.githubusercontent.com/31877486/138051362-026422d1-7f5a-4a8b-9993-4b85c76939c9.png> Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#983>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA653HQW4VGFTVYMHXMIMNLUHZY4ZANCNFSM5GK62GPA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

   Reacted by Roshan Shrestha and praneen

   Reacted by Roshan Shrestha
2. josemduarte

   added

   questionOpen discussions about the libraryOpen discussions about the library

   on Oct 20, 2021
3. RoshanShrestha123 commented on Oct 21, 2021

   

   RoshanShrestha123

   on Oct 21, 2021

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   Thank you @willishf , 🎉
   I will look into the link you shared.
4. RoshanShrestha123 commented on Oct 22, 2021

   

   RoshanShrestha123

   on Oct 22, 2021

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   I looked into couple of thing you mention @willishf , I believe they are the AWT or Swing based component that render the alignment. I was really looking for the class that can return the alignments as the "Text" so that i can return it to the frontend application( of different stack) via API call and render their instead. Thanks
5. aalhossary commented on Oct 22, 2021

   

   aalhossary

   on Oct 22, 2021

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   Hello @RoshanShrestha123 You are welcome to extract the text based rendering and share it to (current) BioJava.
   Alternatively, you may request it to be ported to BioJava and provide the ability to expose the text alignment. But the drawback of this approach is that you will have to wait until of the developers have time to do it for you.
   I may have time in December if you want.

   Reacted by Roshan Shrestha
6. sbliven commented on Jan 4, 2022

   

   sbliven

   on Jan 4, 2022

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   @RoshanShrestha123 Take a look at SimpleProfile.toString(StringFormat). In particular, maybe the PDBWEB format would work for you. It outputs an HTML DIV like

         seq 2 ERNDKK 7
                || | |
         seq 1 ER-DNK 5
   

   Legend: Green - identical residues | Pink - similar residues | Blue - sequence mismatch | Brown - insertion/deletion |

   (legend included, and some css has to be defined appropriately to enable colors).

   If you really want to match the text output above, this can either be implemented as a new Profile.StringFormat (easy but needs a BioJava PR) or you can do it in app code.
7. sbliven

   added a commit that references this issue on Jan 27, 2022

   Temporary commit. Needs to be amended!

   a4006f0
8. sbliven commented on Jan 27, 2022

   

   sbliven

   on Jan 27, 2022

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   I started working on this, thinking it would be an easy fix. However there are some things I need to clarify about how the StringFormat methods are intended to work (see separate issue). There are some commits in sbliven/biojava-sbliven/fix983 which will need to be ammended and rebased. However ProfileFormatTest.java has a method for printing the desired format in BioJava 6.0.

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