It looks good Jan!
I like the StructConsensus chart. That’ll be really useful. One thing I’d like to see when I colour the alignment by RNA helices, is the inconsistent positions highlighted in flashing red (or, similar to Ralee - just not highlighted). This really helps to identify problem areas in an alignment.
The structure consensus logo view is an interesting way to go. I would’ve thought there wasn’t enough room for displaying both residues of a pair in each column but on my big monitor it actually seems to work well.
I like the integration with VARNA and the flipping between the alignment and squigle plots for a sequence. What is the “trim” view? Is this the constrained refold (RNAfold -C) using the consensus as the constraint? Or is it just the MFE structure?
I’m impressed it all seems to work on my Ubuntu machine. I haven’t figured out how to shuffle gap-blocks around yet - possibly just a case of RTFM.
···
On Wed, Aug 17, 2011 at 02:38, Jan Engelhardt <engelhardt87@googlemail.com> wrote:
Hi everybody,
my summer of code project is coming to an end soon. Therefore I would
highly appreciate for any comments on the current version especially bug
reports.
Of course we are also open for future feature requests.
My versions can still be accessed by the links Jim posted some time ago:
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/jan/webstart/jalview_2G.jnlp
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/jan/webstart/jalview_1G.jnlp
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/jan/webstart/jalview.jnlp
As usual, you can also find all the other build artifacts under
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/jan
Jan
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Hi Paul - thanks for taking the time to check out the code!
It looks good Jan!
I like the StructConsensus chart. That'll be really useful. One thing I'd like to see when I colour the alignment by RNA helices, is the inconsistent positions highlighted in flashing red (or, similar to Ralee - just not highlighted). This really helps to identify problem areas in an alignment.
that sounds like something 'reasonably easy' to do but probably not something Jan can fit in to the GSOC project. It would just involve adding the base pair compatibility test logic to the existing helix colourscheme - however, that might lead to some performance issues, since we don't do the base-pair lookup in a particularly efficient way at the moment.
The structure consensus logo view is an interesting way to go. I would've thought there wasn't enough room for displaying both residues of a pair in each column but on my big monitor it actually seems to work well.
The contact-logo was something that I've wanted to have since I first started looking at RNA with Jalview. We still need to make it easy to quickly increase the column width to make sure the contact is immediately legible - but generally, I'm also pretty pleased with the result.
I like the integration with VARNA and the flipping between the alignment and squigle plots for a sequence. What is the "trim" view? Is this the constrained refold (RNAfold -C) using the consensus as the constraint? Or is it just the MFE structure?
I'll leave Jan to answer this one.
I'm impressed it all seems to work on my Ubuntu machine. I haven't figured out how to shuffle gap-blocks around yet - possibly just a case of RTFM.
Gap blocks ? Not sure if that is in the manual 
- could you tell us a bit more about what you mean ?
Jim.
···
On 17/08/2011 01:03, Paul P. Gardner wrote:
The structure consensus logo view is an interesting way to go. I
would’ve thought there wasn’t enough room for displaying both residues
of a pair in each column but on my big monitor it actually seems to
work well.
The contact-logo was something that I’ve wanted to have since I
first started looking at RNA with Jalview. We still need to make it easy
to quickly increase the column width to make sure the contact is
immediately legible - but generally, I’m also pretty pleased with the
result.
Well it worked well. Have you considered adding mutual information content? It’s a rubbish metric but historically it’s been used for this sort of thing. eg. http://www.cbs.dtu.dk/~gorodkin/appl/slogo.html
I’m impressed it all seems to work on my Ubuntu machine. I haven’t
figured out how to shuffle gap-blocks around yet - possibly just a
case of RTFM.
Gap blocks ? Not sure if that is in the manual - could you tell us a
bit more about what you mean ?
I just wanted to edit the alignment. The mouse controls aren’t working for some reason. However I found the Key Strokes manual here:
http://www.jalview.org/help.html
And now I’m pretty sorted, thanks!
Hi.
Well it worked well. Have you considered adding mutual information content? It's a rubbish metric but historically it's been used for this sort of thing. eg. http://www.cbs.dtu.dk/~gorodkin/appl/slogo.html <http://www.cbs.dtu.dk/~gorodkin/appl/slogo.html>
yes - we should be using some better metrics, and have a couple of directions in mind. Not sure when they'll get implemented, though
I just wanted to edit the alignment. The mouse controls aren't working for some reason. However I found the Key Strokes manual here:
http://www.jalview.org/help.html
And now I'm pretty sorted, thanks!
ah - I thought 'gap blocks' was some RNA technical term I'd not heard of .. doh!
For mouse editing : Shift + click + drag should insert/delete gaps, and if a group of sequences in selected, ctrl+click+drag inserts/deletes gaps in all selected sequences. Sometimes you might not be able to do anything because of the 'locked editing' function (where edits are restricted to just the currently selected region). There's also a feature request about introducing some visual indicators to telegraph to the user what to do / why their edit isn't happening, that I'll get to at some point. If these don't work for you then it might possibly be a bug - of course... in which case, head over to issues.jalview.org.
Jim.
···
On 17/08/2011 10:48, Paul P. Gardner wrote:
Hi Paul,
thank you for your comments about Jalview.
I like the integration with VARNA and the flipping between the
alignment and squigle plots for a sequence. What is the "trim" view?
Is this the constrained refold (RNAfold -C) using the consensus as the
constraint? Or is it just the MFE structure?
I'll leave Jan to answer this one.
I'm currently documenting all this stuff
Unfortunately we did not managed to include external programs to Jalview
during the summer project. This is definitely on our Todo list for
further work.
The "trim" view is the individual sequence folded into the the gap-free
consensus structure. This means all columns that contained gaps in the
individual sequence were removed. If this breaks a base-pair the pairing
is removed also.
Basically this is the cheapest way to get an approximation of the
individual structure but of course it is not necessarily the real one.
best
Jan
Hi,
the new features are now also documented under 'Nucleic Acids support'
in the Jalview documentation. If anybody had problems working with it,
he should take a look.
best
Jan