Hello,
I was wondering if Jalview has a solution already built in for this problem I’ve been having.
We add columns to all rows in Jalview by highlighting the column to the immediate left of the position where columns need to be added, holding down the “Ctrl” key, and using the mouse to right click and drag the column to the immediate right of where the columns need to be added. If there is another method to add columns to all rows, please feel free to let me know.
When we add columns using this method, the annotation line for the secondary structure automatically adds spaces where the new columns were added. At the moment, it doesn’t matter too much. However, when the file is saved as a stockholm and read back into Jalview, the secondary structure gives orange coloring which indicates that the secondary structure information is incorrect.
The current solution to the problem is that when columns are added to all rows in Jalview, the secondary structure must be manually changed by right clicking the annotation and clicking “RNA Helix” to replace all of the spaces with periods ("."). Is it possible for the Jalview program to automatically add periods instead of spaces when columns are added so that the secondary structure doesn’t stop working correctly when saved?
I’m a teaching assistant in Dr. Gutell’s computational biology course at UT Austin. We are trying to reduce the amount of time spent fixing alignments due to these specific insertion issues. Is it possible for this issue to be resolved before classes start at the end of August?
Thanks,
Vaish
Hello Vaish,
We add columns to all rows in Jalview by highlighting the column to the immediate left of the position where columns need to be added, holding down the “Ctrl” key, and using the mouse to right click and drag the column to the immediate right of where the columns need to be added. If there is another method to add columns to all rows, please feel free to let me know.
Apart from keyboard mode (http://www.jalview.org/node/34) this is the only way. Is there a specific reason why you need to perform these kinds of edits frequently ?
When we add columns using this method, the annotation line for the secondary structure automatically adds spaces where the new columns were added. At the moment, it doesn’t matter too much. However, when the file is saved as a stockholm and read back into Jalview, the secondary structure gives orange coloring which indicates that the secondary structure information is incorrect.
This appears to be one cause of the bug you reported earlier in https://issues.jalview.org/browse/JAL-3053 - although in this case, you’ve identified the easiest fix: to insert a ‘.’ rather than a gap in RNA secondary structure annotation rows (which is a trivial patch). I’d still like to resolve the stockholm file ambiguity, however.
I’m a teaching assistant in Dr. Gutell’s computational biology course at UT Austin. We are trying to reduce the amount of time spent fixing alignments due to these specific insertion issues. Is it possible for this issue to be resolved before classes start at the end of August?
This fix could be included in the next patch release for 2.10.4b1. Please sign up at issues.jalview.org and register as a watcher on the bug to track its progress: https://issues.jalview.org/browse/JAL-3061
Happy Jalviewing…
Jim.
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On 03/07/2018 21:07, Vonyx Crystal wrote:
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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)