[Jalview-discuss] question about using DAS service and JalviewLite

[Sai Tong]

>> Yes, Jim,
>> might be I should try to attempt the more obvious approach first.  I 
>> already have the ID mappings made in a backend data warehosue.  This 
>> is not ideal because uniprot ids  and accession numbers can change 
>> from version to version in the long-run. But at least this would help 
>> to do what I want to do with displaying sequence feature annotations 
>> within JalviewLite for now.
> yes. that's going to be the quickest way. However, if you make sure 
> that you use properly versioned uniprot accessions then it should 
> always be possible to recover the annotation - if not from the current 
> uniprot DAS service, then via the uniparc services (though I haven't 
> tried this).
>
>> In regarding to the missing "sequence conservation, quality and 
>> consensus plot" from JalviewLite, I think perhaps it might have to do 
>> with the number of sequences I have in the .aln file that I used to 
>> visualize with JalviewLite.  In the example I gave previously, there 
>> were 288 sequences in the MSA,  and if I select "Show Annotations" 
>> from "View" drop-down menu in JalviewLite, I don't see those 3 plots 
>> appear. However, if I open a full-version of Jalview using Java Web 
>> Start, I am able to see the 3 plots beneath the sequence alignment 
>> window.   Is there a limit of how many sequences that JalviewLite can 
>> visualize in addition to showing the "sequence conservation, quality 
>> and consensus plot for the alignment"?
> The wrapped mode is limited by the vertical size of the screen. Both 
> the applet and application have this problem when there are very large 
> numbers of sequences. If you reduce the font size (hold down the 
> middle mouse button and drag towards the top left) then you will see 
> that the conservation, consensus and quality plots are rendered - but 
> fall off the bottom of the screen if the font is too big. This is one 
> of the aspects which Albert is interested in fixing via the 'Google 
> map Jalview' project.
Thanks Jim, yes, your suggestion of adjusting the font size is right on .
Aligning large number of sequence definitely makes it difficult, if not 
impossible,  for users to use Jalview to look through the alignment at 
different resolution level.    

-Sai


>
> Jim.
>