[Jalview-discuss] annotation for nucleotide alignments

[Jim Procter]

Hi Stephanie - thanks for resending your email.

On 18/03/2010 16:26, Stephanie Blandin wrote:
> I'm trying to color a nucleotide alignment by annotation (conservation in this case), so that only the non conserved nucleotides are highlighted in color. See attached document below for an idea of what I need.
understood.
> I managed to do it previously (I was working with a previous version of Jalview - v9 I believe for macs - but I am not sure the issue comes from that).
> Now, I'm trying to do the same with another alignment and with Jalview v10,
whoa.. can I ask you where you have got these version numbers from ?  
The current version of the application available from 
http://www.jalview.org/download.html is 2.4.0b2 - and assuming that you 
are using the Jalview Desktop application, you should be able to see 
this in the 'About' dialog box available from the Desktop window's Help 
menu.
> but it is not possible to select the option "by conservation" (and the accompanying "Modify Conservation Threshold..."), and when I select the option "by annotation", the window that pops up is empty.
There are a number of things that may cause this:

1. Make sure you have the 'caculate consensus' preference enabled - 
otherwise Jalview will not automatically calculate any consensus 
annotation for the alignment. To do this, open the 'preferences' dialog 
(under the Desktop's Tools menu) and check that the box next to 
'consensus' is ticked (if it isn't, tick it, click ok, and then reload 
your alignment).

2. are you working with a very big alignment ? if so, then you may have 
run out of memory - jalview will give up trying to calculate the 
consensus histogram if there are too many sequences. Check the 'Show 
memory usage' box under 'Tools' to see if you are low on memory. - and 
have a look at the faq entry to see how to increase it if you have less 
than 50% left with just one alignment loaded ( 
http://www.jalview.org/faq.html#incmemory ).

3. there is a remote possibility that you are using one of the mac java 
versions which Jalview doesn't play well with. Check the java settings 
on your machine to make sure you are using a java 1.6 virtual machine 
(see this post, for instance: 
http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/2009-March/000164.html 
).

I'm hoping that #1 provides the answer to this problem, or if not - #2 
is the cause. #3 is an outside bet, but you would be having many other 
problems if you are using an incompatible JVM. Please let me know if 
none of these fix the problem!

best of luck..
Jim.

-- 
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J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.