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Wednesday, August 18, 2010

Demonstration of GSoC Project

The features that developed for the GSoC project will be available in the next Jalview release. You can also contact me and I can send you a jar file with the new features, or download the code from the Google code hosting page for Jalview and see my post on how to set up Eclipse with Jalview. The code submitted to Google is the same as rev 32 on the Google code host site.

Addendum: Jim posted a comment with a link to the webstart version.


  1. You can fetch sequences from RFAM via the sequence fetcher. Go to "File > Fetch Sequence(s)..." and a dialog box will appear.


  2. From the database drop down menu select RFAM (Full) for the "Full" alignment from RFAM or RFAM (Seed) for the "Seed" alignment. Seed alignments are the original alignments constructed to create a covariance model for searching databases. Full alignment are the result of a search using the covariance model against the sequence database. For this demonstration, I used RFAM (Seed), but selecting the RFAM (Full) will be very similar.

  3. Click the "Example" button to load an alignment name. Click the "OK" button to fetch the alignment.


  4. A new dialog box will appear with the alignment. The RFAM sequence fetcher retrieves files in Stockholm format, so Jalview can interpret the secondary structure information in the file. The secondary structure information in the file is displayed in WUSS notation and helices that are determined from this information are displayed as blue arrows in the Annotation panel.




  5. You can color the helices with the "By RNA helices" color option. Go to "Colour > By RNA helices."


  6. The helices should now be colored.


  7. To view the consensus logo in the Annotation panel, go to "View > Autocalculated Annotation > Show Consensus logo". The coloring of the logo will change based on which color scheme is selected.


  8. Close up of Consensus logo when "By RNA helices" or "Purine/Pyrimidine coloring is selected.




  9. To change the color scheme to "Purine/Pyrimidine" go to "Colour > Purine/Pyrimidine"




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