iPUP

iPUP based on the composition of k-spaced amino acid pairs and support vector machines is a tool for computational identification of pupylated proteins and pupylation sites. iPUP provides an easily accessible web service and a standalone software. The model of iPUP is trained on the dataset extracted from PupDB, a database of pupylated proteins and pupylation sites (link to PupDB).


[Back to content]

How to submit a protein to iPUP web server for prediction of pupylation sites

  • Step 1. Prepare your protein sequence using FASTA format

    • This is an example protein sequence of FASTA format
    >P96382
MTFPGDTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDD
YAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQ
ELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTT
LTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGASSVFVNYDGTSKRRTTVGSHV
RTGSDTMFVAPVTIGDGAYTGAGTVVREDVPPGALAVSAGPQRNIENWVQRKRPGSPAAQASKRASEMACQQPTQPPDADQTP

  • Step 2. Enter the protein sequence into the textbox (including header ">P96382") and click "Click to predict pupylation sites"




  • Step 3. Results will be shown in the web page




  • Step 4. Header of table is clickable for sorting

    • Also, there is a green link "Download as csv file". Users can download the prediction results for analysis.



    [Back to content]

    How to interpret the result of iPUP

    Given a protein sequence, the lysines (k) will be encoded as a modified composition of k-spaced amino acid pairs (MAAP). Subsequently, prediction results and probabilities will be shown in the web page. A set of pre-defined thresholds of High, Medium and Low is utilized to classify input lysines into four categories as follows. The thresholds are defined according to the specificity level of 10-fold cross-validation. Threshold values of High, Medium and Low are corresponding to specificity of 90%, 85% and 80%. Users can either use the pre-defined thresholds or define their own thresholds to classify lysines.

    ScoreProbability of being a pupylation site
    0.1167 < scorePupylation site(High)
    0.1044 < score < 0.1167Pupylation site(Medium)
    0.0963 < score < 0.1044Pupylation site(Low)
    score < 0.0963Non-pupylation site


    [Back to content]

    How to use iPUP software for prediction of pupylation sites

  • Step 1. Prepare your protein sequence using FASTA format

    • This is the content of an example file
    Click to download example sequence file 
    >P96382
MTFPGDTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDD
YAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQ
ELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTT
LTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGASSVFVNYDGTSKRRTTVGSHV
RTGSDTMFVAPVTIGDGAYTGAGTVVREDVPPGALAVSAGPQRNIENWVQRKRPGSPAAQASKRASEMACQQPTQPPDADQTP
>A0QPN2
MSYTAADITELDDVQHTRLRPAVNLGLDVLNTALREIVDNAIEEVADPGHGGSTVTITLHADGSVSVADDGRGLPVDTDPTTGKNGIVKTLGTARAGGKF
SAHKDATSTGAGLNGIGAAAAVFISARTDVTVRRDGKTFLQSFGRGYPGVFEGKEFDPEAPFTRNDTQKLRGVSNRKPDLHGTEVRILFDPAIAPDSTLD
IGEVLLRAHAAARMSPGVHLVVVDEGWPGEEVPPAVLEPFSGPWGTDTLLDLMCTAAGTPLPEVRAVVEGRGEYTTGRGPTPFRWSLTAGPAEPATVAAF
CNTVRTPGGGSHLTAAIKGLSEALAERASRMRDLGLAKNEEGPEPQDFAAVTALAVDTRAPDVAWDSQAKTAVSSRSLNLAMAPDVARSVTIWAANPANA
DTVTLWSKLALESARARRSAEGAKARARAASKAKGLGTNLSLPPKLLPSRESGRGSGAELFLCEGDSALGTIKAARDATFQAAFPLKGKPPNVYGFPLNK
ARAKDEFDAIERILGCGVRDHCDPELCRYDRILFASDADPDGGNINSSLISMFLDFYRPLVEAGMVYVTMPPLFVVKAGDERIYCQDESERDAAVAQLKA
SSNRRVEVQRNKGLGEMDADDFWNTVLDPQRRTVIRVRPDESEKKLHHTLFGGPPEGRRTWMADVAARVDTSALDLT

  • Step 2. Download and open iPUP"

    • In [File], you can choose [Open] to open the saved file.

    Or you can use [Help]->[Load sample Sequence]



  • Step 3. Results will be shown in the table

    • Then, you can choose [All]/[High]/[Medium]/[Low]/[User defined] threshold to filter pupylation sites.

  • Step 4. Save your results in a csv file




    • [Back to content]

    How to cite iPUP

    If you find iPUP useful. Please cite:
    Tung, C.-W. (2013) Prediction of pupylation sites using the composition of k-spaced amino acid pairs, Journal of Theoretical Biology.


    [Back to content]