https://github.com/fjossinet/assemble2

Assemble2 allows you to design your RNA 2D structure interactively and to create and assemble the corresponding RNA 3D modules directly in UCSF Chimera
https://github.com/fjossinet/assemble2

bioinformatics java pdb rna rna-structure visualization

Last synced: 2 months ago
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Assemble2 allows you to design your RNA 2D structure interactively and to create and assemble the corresponding RNA 3D modules directly in UCSF Chimera

• Host: GitHub
• URL: https://github.com/fjossinet/assemble2
• Owner: fjossinet
• Created: 2016-07-07T08:47:46.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2018-01-25T07:48:19.000Z (almost 7 years ago)
• Last Synced: 2024-04-24T02:08:23.310Z (9 months ago)
• Topics: bioinformatics, java, pdb, rna, rna-structure, visualization
• Language: Java
• Homepage: https://fjossinet.github.io/assemble2/
• Size: 30.9 MB
• Stars: 4
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Assemble2: visualize, construct and study RNA architectures

Main features:

* Assemble2 allows you to visualize and edit RNA structures described in a file (CT, BPSep, FASTA, PDB) or recovered from databases (RFAM, PDB, SSTRAND).

* Assemble2 provides a panel dedicated to the dispaly and the interactive manipulation of an RNA secondary structure (2D).

* if the 2D is derived from a solved 3D, Assemble2 can load this 3D into to the viewer [UCSF Chimera](http://www.cgl.ucsf.edu/chimera/).

* Assemble2 keeps a link between the two structures, making the 2D a guide in the exploration of the solved 3D.

* this link makes also the 2D a guide for the construction of a new 3D. Each selection in the 2D can be used to query a database of 3D fragments to be assembled into a 3D model.

* Assemble2 is connected to RNA algorithms and databases made available as Web Services from a cloud in order to automate recurrent tasks of a working session:

  * 2D prediction from an RNA primary sequence

  * 2D annotation from an RNA tertiary structure

  * 2D plot of a secondary structure

  * query of 3D fragments from a 2D selection

Assemble2 has been developed with the Java language on MacOSX. It has been tested on MacOSX and Linux Ubuntu. But it should run on any operating system having a Java environment.

![Assemble2 description](media/poster-assemble2.png)

* [Documentation](https://github.com/fjossinet/assemble2/wiki)

* [Download and installation](https://github.com/fjossinet/assemble2/wiki/Download-and-installation)