DeepGOWeb Protein Function prediction webserver


DeepGOWeb is a webservice for predicting protein functions based on protein sequence using DeepGOPlus method. It uses deep convolutional neural networks to learn sequence features and combines predictions with sequence similarity based predictions.

The tool only needs protein sequence as an input. The source code of the model is available on GitHub repository

The REST API is available for submitting sequences programmatically.

We also provide a SPARQL endpoint for calling our predictor in SPARQL queries.

Input data:

  • Format: FASTA format or Raw Sequences separated by a newline
  • Threshold: a value between 0.1 and 1.0 for filtering predictions by the confidence score of the model
  • Data: Protein sequences in selected format


The number of sequences in one query should not exceed 10!

Examples:

Output description:

The output page provides function predictions for each protein. A prediction includes GO terms for the Biological Process, Molecular Function, and Cellular Component sub-ontologies with confidence scores. Only predictions with a confidence above the threshold parameter are shown. We also show a list of proteins that are used for predictions based on sequence similarity and their similarity score to the query protein. The results are provided under the CC-BY License and can be downloaded in JSON/CSV formats. You can find an example output here and a more detailed description of the information generated by DeepGOWeb in the Documentation.

>sp|P80386|AAKB1_RAT 5'-AMP-activated protein kinase subunit beta-1 OS=Rattus norvegicus GN=Prkab1 PE=1 SV=4 MGNTSSERAALERQAGHKTPRRDSSGGTKDGDRPKILMDSPEDADIFHTEEMKAPEKEEF LAWQHDLEVNEKAPAQARPTVFRWTGGGKEVYLSGSFNNWSKLPLTRSQNNFVAILDLPE GEHQYKFFVDGQWTHDPSEPIVTSQLGTVNNIIQVKKTDFEVFDALMVDSQKCSDVSELS SSPPGPYHQEPYISKPEERFKAPPILPPHLLQVILNKDTGISCDPALLPEPNHVMLNHLY ALSIKDGVMVLSATHRYKKKYVTTLLYKPI


MPYKLKKEKEPPKVAKCTAKPSSSGKDGGGENTEEAQPQPQPQPQPQAQSQPPSSNKRPSNSTPPPTQLSKIKYSGGPQIVKKERRQSSSRFNLSKNRELQKLPALKDSPTQEREELFIQKLRQCCVLFDFVSDPLSDLKFKEVKRAGLNEMVEYITHSRDVVTEAIYPEAVTMFSVNLFRTLPPSSNPTGAEFDPEEDEPTLEAAWPHLQLVYEFFLRFLESPDFQPNIAKKYIDQKFVLALLDLFDSEDPRERDFLKTILHRIYGKFLGLRAYIRRQINHIFYRFIYETEHHNGIAELLEILGSIINGFALPLKEEHKMFLIRVLLPLHKVKSLSVYHPQLAYCVVQFLEKESSLTEPVIVGLLKFWPKTHSPKEVMFLNELEEILDVIEPSEFSKVMEPLFRQLAKCVSSPHFQVAERALYYWNNEYIMSLISDNAARVLPIMFPALYRNSKSHWNKTIHGLIYNALKLFMEMNQKLFDDCTQQYKAEKQKGRFRMKEREEMWQKIEELARLNPQYPMFRAPPPLPPVYSMETETPTAEDIQLLKRTVETEAVQMLKDIKKEKVLLRRKSELPQDVYTIKALEAHKRAEEFLTASQEAL