Hi everyone,
I am using a Python alignment program where I call for a jalview batch in order to have as output svg images with the result of my alignments.
I followed the instruction I found in these web-pages:
http://www.jalview.org/node/40
http://www.jalview.org/help/html/features/clarguments.html
I would like to have in the images also the SECONDARY STRUCTURE ANNOTATION and THE LOGO on CONSENSUS HISTOGRAMS.
I can’t figure out how to do this…
I am thinking that maybe I would have to add some parameters in the Jalview properties file.
Does someone know how to do this? Which the appropriate commands are?
Thanks!
Alessandra
Hello Alessandra
I would like to have in the images also the SECONDARY STRUCTURE ANNOTATION and THE LOGO on CONSENSUS HISTOGRAMS.
I can't figure out how to do this...
I am thinking that maybe I would have to add some parameters in the Jalview properties file.
You're correct, though you may also need some additional data: since you can only display secondary structure annotation if you actually have some secondary structure information for sequences. Jalview can extract those data automatically from 3D structure, but to do that you'll need to have the PDB files available for your sequences. Alternately, if you have secondary structure annotation, you could turn them into Jalview annotation files. Which do you prefer here ?
Modifying the properties to get the layout/visualisations you need for batch mode.
The easiest way to do this is to launch Jalview in interactive mode with the '-props' argument pointing to a copy of your current jalview properties file. Then configure the default annotation options via Tools->Preferences so that consensus sequence logos are displayed automatically.
For what you want, though - the relevant property line for showing consensus logos is:
SHOW_CONSENSUS_LOGO=true
Let me know what you want to do about secondary structure annotation... if you have annotation available it might be easiest to create an importer with a groovy script.
Jim.
···
On 15/06/2015 12:51, Alessandra Gastaldello wrote:
Hello Jim,
thank you for your explanations! Now I am able to display consensus logo.
In regard to secondary structures, i don’t have neither PDB files nor secondary structure annotations…
Since for the moment our program aligns all protein sequences (selected for a certain modification) it can found on a web site, we have not thought to include secondary structure information, and we thought this was something “automatic” for jalview (to find in web secondary structure). Anyway, we are thinking how to modify our program to include secondary structure.
As soon as we will have either PDB or annotation I think I will come back to you…
In the meanwhile, thank you again.
Alessandra
···
2015-06-15 20:16 GMT+02:00 Jim Procter <jprocter@compbio.dundee.ac.uk>:
Hello Alessandra
On 15/06/2015 12:51, Alessandra Gastaldello wrote:
I would like to have in the images also the SECONDARY STRUCTURE
ANNOTATION and THE LOGO on CONSENSUS HISTOGRAMS.
I can’t figure out how to do this…
I am thinking that maybe I would have to add some parameters in the
Jalview properties file.
You’re correct, though you may also need some additional data: since you
can only display secondary structure annotation if you actually have
some secondary structure information for sequences. Jalview can extract
those data automatically from 3D structure, but to do that you’ll need
to have the PDB files available for your sequences. Alternately, if you
have secondary structure annotation, you could turn them into Jalview
annotation files. Which do you prefer here ?
Modifying the properties to get the layout/visualisations you need for
batch mode.
The easiest way to do this is to launch Jalview in interactive mode with
the ‘-props’ argument pointing to a copy of your current jalview
properties file. Then configure the default annotation options via
Tools->Preferences so that consensus sequence logos are displayed
automatically.
For what you want, though - the relevant property line for showing
consensus logos is:
SHOW_CONSENSUS_LOGO=true
Let me know what you want to do about secondary structure annotation…
if you have annotation available it might be easiest to create an
importer with a groovy script.
Jim.
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
Hi Alessandra.
It’s probably better to discuss off list - since we’re getting into details of your program, but I suspect you might be most interested in visualising secondary structure as sequence features on the alignment. One way to do this would be to prepare a GFF file containing all Uniprot secondary structure annotation and add a '-features ’ command line argument (see http://www.jalview.org/help/html/features/featuresFormat.html for how to add colour/shading specifications for features).
There are also web services that Jalview can access (either Uniprot directly or DAS services)but since you are running a server you may not want Jalview to be querying web services to retrieve annotation.
Jim.
···
On 16/06/2015 10:43, Alessandra Gastaldello wrote: