Hub
Pricing About
  • Software
  • Blog
  • Forum
  • Events
  • Documentation
  • About KNIME
  • KNIME Community 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
Temesgen Dadi profile image

Last edited: 

Drag & drop
Like
Download workflow
Copy short link
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
  • Go to item
    KNIME Base nodes Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.3

    knime
  • Go to item
    KNIME Deep Learning - Keras Integration Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.1

    knime
  • Go to item
    KNIME Expressions Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.2

    knime
  • Go to item
    KNIME JavaScript Views Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.3

    knime
  • Go to item
    KNIME JavaScript Views (Labs) Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.2

    knime
  • Go to item
    KNIME Javasnippet Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.0

    knime
  • Go to item
    KNIME Quick Forms Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.2.3

    knime
  1. Go to item
  2. Go to item
  3. Go to item
  4. Go to item
  5. Go to item
  6. Go to item
Loading deployments
Loading ad hoc executions

Legal

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

Discussion
Discussions are currently not available, please try again later.

KNIME
Open for Innovation

KNIME AG
Talacker 50
8001 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 Business Hub
© 2023 KNIME AG. All rights reserved.
  • Trademarks
  • Imprint
  • Privacy
  • Terms & Conditions
  • Credits