Hub
  • Software
  • Blog
  • Forum
  • Events
  • Documentation
  • About KNIME
Sign in
  • KNIME Hub
  • temesgen-dadi
  • Spaces
  • Public
  • Example_Workflows_for_Components
  • DS-363_Example_WF_for_One-Hot_Encoder_Component
WorkflowWorkflow

Example Workflow for One-Hot Encoder (Biological Sequences) Component

bioinformatics deep learning one-hot encoding sequencing RNA

Last update: 

Drag Workflow
Workflow preview
In this example workflow we demonstrate the usage of One-Hot Encoder (Biological Sequences) component which is part of the KNIME Verified Components (https://www.knime.com/verified-components). After reading FASTA files using another verified component created for this purpose, we pass the table containing cDNA sequences to the One-Hot Encoder component which turns the sequences to one-hot encoded vectors. We use these one-hot encoded vectors to train a deep learning network (CNN) created using the KNIME keras integration. The data contains cDNA sequences where some of these sequences represent RNAs that are binding preferences to ELAVL1A protein. The model is trained and to predict if a sequence is a binding preference for this particular protein or not. The data used in this workflow are from the following publication: Xiaoyong Pan, Peter Rijnbeek, Junchi Yan, Hong-Bin Shen. Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks. BMC Genomics, 2018, 19:511. Specifically: https://github.com/xypan1232/iDeepS/tree/master/datasets/clip

External resources

  • One-Hot Encoder (Biological Sequences) Component
  • FASTA Reader Component
  • KNIME Verified Components

Used extensions & nodes

Created with KNIME Analytics Platform version 4.2.3
  • KNIME Base nodes Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.3

  • KNIME Deep Learning - Keras Integration Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.1

  • KNIME Expressions Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.2

  • KNIME JavaScript Views Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.3

  • KNIME JavaScript Views (Labs) Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.2

  • KNIME Javasnippet Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.0

  • KNIME Quick Forms Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.3

Legal

By downloading the workflow, you agree to our terms and conditions.

License (CC-BY-4.0)
Short link
Discussion
Discussions are currently not available, please try again later.

KNIME
Open for Innovation

KNIME AG
Hardturmstrasse 66
8005 Zurich, Switzerland
  • Software
  • Getting started
  • Documentation
  • E-Learning course
  • Solutions
  • KNIME Hub
  • KNIME Forum
  • Blog
  • Events
  • Partner
  • Developers
  • KNIME Home
  • KNIME Open Source Story
  • Careers
  • Contact us
Download KNIME Analytics Platform Read more on KNIME Server
© 2021 KNIME AG. All rights reserved.
  • Trademarks
  • Imprint
  • Privacy
  • Terms & Conditions
  • Credits