[Jalview-discuss] annotation for nucleotide alignments

[Jim Procter]

Hi Stephanie.

On 19/03/2010 10:17, Stephanie Blandin wrote:
> Thanks very much for your quick answer!
>    
no probs.
>
> Well, sorry about that. It is indeed the latest Desktop version I am using on a Mac (OS 10.6.2). When I open Jalview, it says 2.4.0.b2, but if I choose "About Jalview" in the Jalview menu next to the apple on the upper menu bar, it says v10 ;-)
>    
ah. hmm. I'll have to take a close look at where that comes from. I 
don't remember seeing that on my own 10.6 install.

> The "autocalculate consensus" was indeed enabled. The "conservation" box is also checked in preferences/visual/open new alignment, and actually, it works very well when I open an amino acid alignment: I do see the conservation annotation when working with aa aln, and I can color my alignment by annotation/conservation then.
>    
That's good. I should say here that the reason you don't see a 
conservation trace for the nucleotide alignment is because the 
conservation calculation is based on amino acid chemical property 
conservation - so its disabled when working with nucleotide alignments. 
However, you should still see the consensus trace (and be able to use it 
via the 'colour by annotation' dialog). One thing that affects the 
consensus calculation is whether there are lage deletions in many of the 
sequences - if this is the case with your particular alignment then 
right click on the consensus row to enable the 'ignore gaps' option.

> I checked this and it is fine. The specific aln I was working with include 2-6 sequences, up to 5kb or so. There is more than 70% of free memory.
>    
ok. definitely no problems there at all.
>> 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
>> ).
>>      
> The Java version I have is 1.6.0_17 from Apple Inc. (it includes a 32-bit and a 64-bit version of Java SE6). And the rest of the tools/window sizing/etc that I have tested work well.
>    
again, no problems.

> I could try to open my aln on a different computer equipped with an older version of Jalview. I'll keep you updated.
>    
that might help you - but I'd like to get to the bottom of this since it 
looks like the 2.4.0b2 version of jalview is working fine - but 
apparently not letting you do what you want. If the above comment about 
the consensus annotation doesn't help then would it be ok if you sent me 
an alignment that demonstrates the problem ?

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.