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

[Jim Procter]

On 13/03/2010 01:04, Sai Tong wrote:
>>
>>>
>>> The real problem is that I really should/want to get the uniprot 
>>> sequence feature annotations and let JalviewLit be able to visualize 
>>> the features.  The problem is my current aln  files do not contains 
>>> sequences with uniprot ids as their names. Even though I have the 
>>> map to map from the uniprot id to the 13-character-name found in the 
>>> aln file,  I might still have to modify the sequence feature 
>>> information from  uniprot and re-name the protein name into the ones 
>>> match with the names found in my aln files in order for the feature 
>>> annotation to appear for the sequences in the MSA in jalview.
>> I see. Basically you want the full ID mapping functionality in the 
>> jalview desktop accessible from the applet. There are several routes 
>> you can take here: the most obvious one is to warehouse the ID 
>> mappings beforehand within a small web service and roll your own 
>> client side lookup to translate IDs before doing the DAS request, the 
>> other extreme would be to develop a java servlet that uses methods in 
>> the jalview package to do the ID lookup, DAS feature retrieval, and 
>> GFF translation for the applet. The latter would  be a very 
>> interesting project - since its effectively creating a client/server 
>> version of Jalview - but would definitely require collaboration to 
>> ensure the internal APIs in Jalview are up to the job.
>
> 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.

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
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