SLiMPred fail to retrieve png/pdf file

[joaoport...@gmail.com]

Hi everyone,

I've tried the SLiMPred tool to run an analysis on Q9VQS4_DROME. It appears to go through the iterations, but in the end I cannot download the pdf file or get access to any of those links that appear in the top left corner. The error only happens for this specific UniProt entry (i've tried different proteins and it worked fine). Is it a bug? How can I get the pdf file with all the info?

Thank you for your time.

Best regards,

Joao

[denis]

Hi Joao

Yes. There is a problem with that sequence. Niall reckoned it is because the sequence may have been updated since 

the alignments on our server was done, creating some kind of incompatibility.  We haven't currently the capacity to review and update all our

alignments in a reasonable timeframe so here's a work-around...

I tried to work off a different alignment set used in the Proviz tool (slim.ucd.ie.proviz) by pasting in the slimpred results from there.

That works well, EXCEPT that the pdf (attached) doesn't have the slimpred track that I can see onscreen (see the word file I attached with images in it), got to try and sort that bug.

If you try the proviz software and enter the upload data option with the attached .csv you should get the software to visualised the slimpred predictions

on your protein. (I edited in the slimpred data that the bioware server returns into the relevant column). 

I know this is a messy work around but if you go into proviz and play with the settings there online hopefully you'll find an image thats useful to you.

If it happens for another protein perhaps you can edit the csv file attached changing the fields as necessary (should be just the two fields called entry number and

position (both usually set to the amino acid position) and the value field set to the SLiMPRED score.

Hope this helps!

All the best

Denis 

[joaoport...@gmail.com]

Hi Denis,

Thanks for your reply and all the work to solve this out. I tried the ProViz software, but it only shows comparison with another specie and I was looking for a more complete alignment analysis. 

I tried to run SLiMPred/ProViz for the human protein and it worked, but only aligns sequences from chordata. Maybe this is a silly question, but is it possible to manually add an extra layer with the Drosophila protein sequence?  

Again, thanks for the help.

Best regards,

Joao

[Denis Shields]

Hi Joao

You can select Arthropoda instead of QFO from on of the top right options which gives you a more informative alignment but not out to mammals (as the name suggests).

That may be enough for you. 

There is a way I think to get manual  alignments: if you have a fasta alignment you can upload it through the alignment tab from the front page

http://slim.ucd.ie/proviz/  make sure drosophila is the FIRST sequence, and then add in the slimpred file to that and hopefully it will work. 

Check it carefully though as this is not supported for full functionality yet and may have some bugs (make sure the residues and the slimpred data seem to line up). 

Denis 

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[joaoport...@gmail.com]

Hi Denis,

Ok, i will try what you are suggesting and hopefully i will get what i am looking for.

Thanks a lot for the help.

Best regards,

Joao 

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