Pon_P3

Citing PON-P3

    PON-P3 was developed by Muhammad Kabir and Mauno Vihinen. Manuscript describing the method has been submitted. Submitted...

    In the meantime, cite the URL of the predictor.

Start prediction

There are two input methods: interactively via a text box or by uploading a file. The platform offers three interfaces for processing data:

  1. Protein variation
  2. Transcript variation
  3. Genomic variation

Each of these interfaces requires inputs in a specific format, variations have to be described in MANE-compliant references. Results are provided with e-mail in both text and PDF formats.

Input protein variation

You can input data via the text box by first entering refseq_ids followed by a ">" symbol. There one or several variation_ids are provided. For uploading a file, the file must contain two columns with header names as refseq_ids and variation_ids. Please refer to the format examples below:

Example

  1. Protein sequence variation
    2. >NP_000005.3
V1292F
W436E
>NP_000008.1
Y382W
S412N

Input transcript variation

Use either the box where transcript varitiations can be pasted or typed or download the example file and make a similar file for submission via a file.

Example

  1. Input transcript variation
    2. NM_000016.6:c.613G>C
NM_000016.6:c.653C>G
NM_000017.4:c.319C>T

Input genomic variation

Use either the box where genomic varitiations can be pasted or typed or download the example file and make a similar file for submission via a file.

Example

  1. Input genomic variation
    2. chr1:g.75745819G>C
chr2:g.47789620T>A
chr3:g.12156789A>G

Datasets

Datasets were obtained with extensive data mining.

Dataset type variations Pathogenic Benign
Training dataset 11567 11478 23045
Blind Test dataset 2581 1246 1335

Training dataset can be download from here. Download

Blind Test dataset can be download from here. Download

PON-P3 excluded 400 protein IDs for which we do not provide results. These proteins did not have all the necessary data available. Download

All predictions from PON-P3 are available for download in a single file. Download

Contact

If you have any problems, please contact Muhammad Kabir (muhammad.kabir@med.lu.se) or Prof. Mauno Vihinen (mauno.vihinen@med.lu.se).