Web Service Tutorial

The functions of the web service:

  1. Overview
  2. Rank Predictions
  3. Generate & Rank Predictions
  4. Infer Interpretability
  5. Result History
  6. Result page

Overview

  1. Home

    Back to the "Home" page.
    Example Page

    We provide a sample result generated by the "Generate & Rank Predictions" function.
    Tutorial

    This page, users can learn how to use this service.
    Contact

    The information about us and the term of use.
  2. Rank Predictions

    Rank the List of Predicted Structures Based on Functional Interpretability
  3. Generate & Rank Predictions

    Generate the Functionally Interpretable Predictions for a Given Sequence
  4. Infer Interpretability

    Infer the Functional Interpretability of a Given Structure
  5. Result History

    Help users to use job_id to find their previously submitted results.

Rank Predictions

In this page, users can upload a .zip file of .ct files to rank the list of predicted sructures based on functional interpretability.

  1. Input: Predicted Structures

    Users can provide a list of structures in the fasta format.
  2. Input: Upload

    Users can also upload your .zip file of .ct files as the input structures.
  3. Input: Species Under Consideration

    Since the implemented prediction ranking algorithm considers species-specific functionality, targeted species should be chosen. In the current version, SSRTool provide the species of Arabidopsis, human, mouse, rat, yeast and zebrafish for users.
  4. Input: Significance level of functional interpretability

    Set the significance level of functional interpretability.
  5. Input: Mail (Optional)

    Depending on the workload of the server, it may take several minutes perform the job.
    Users can optionally provide their mail addresses. A notification letter will be sent when the job is ready.

Generate & Rank Predictions

In this page, users can input the RNA sequence of interest for structure prediction and ranking.

  1. Input: Sequence

    Users can provide the sequence of interest in .fasta format.
    2. Sample Sequence

    Two sample sequences are provided for exploring the web service.
  2. Input: Upload

    Users can also upload the existing .fasta file.
  3. Input: Species

    Since the implemented prediction ranking algorithm considers species-specific functionality, targeted species should be chosen. In the current version, SSRTool provide the species of Arabidopsis, human, mouse, rat, yeast and zebrafish for users.
  4. Input: Significance level of functional interpretability

    Set the significance level of functional interpretability.
  5. Input: Select Structure Prediction Tools

    Select the structure prediction tools to be used in the prediction process.
  6. Input: Mail (Optional)

    Depending on the workload of the server, it may take several minutes perform the job.
    Users can optionally provide their mail addresses. A notification letter will be sent when the job is ready.

Infer Interpretability

Users can input the RNA structure or upload the .ct file to infer the functional interpretability of it.

  1. Input: Structure

    Users can provide the structure of interest in the Dot Bracket File format.
    2. Sample Sequence

    Two sample structures are provided for exploring the web service.
  2. Input: Upload

    Users can also upload the structure .ct file as the input structure.
  3. Input: Species Under Consideration

    Since the implemented prediction ranking algorithm considers species-specific functionality, targeted species should be chosen. In the current version, SSRTool provide the species of Arabidopsis, human, mouse, rat, yeast and zebrafish for users.
  4. Input: Significance level of functional interpretability

    Set the significance level of functional interpretability.
  5. Input: Mail (Optional)

    Depending on the workload of the server, it may take several minutes perform the job.
    Users can optionally provide their mail addresses. A notification letter will be sent when the job is ready.

Result History

You can use the provided Job_id to find the identified RNA functionally interpretable structure ensemble in this page.

  1. Input: Job_ID

    Type in the given Job_ID to find the result.

Result page of "Rank Predictions"

The rankings of the list of predicted structures based on functional interpretability for the given sequence will be summarized in this page.

  1. Job_ID

    The web service Job_ID.
  2. Parameters

    The user-specified algorithm parameters use to rank predictions.
  3. The Meta-stable Structure

    The suggested most native-like candidate structure form the given conformation predictions.
    • (a) Structure: The meta-stable structure can be visualized or downloaded by clicking the provided link.
    • (b) Best Functional Significance: The minimum significance in the functional interpretability metrics.
    • (c) Significance metrics: The functionally interpretability test results of the meta-stable structure.
  4. Prediction Significance Ranking

    The functional rankings of the provided list of structure predictions.
  5. Structure

    The predicted structure can be visualized or downloaded by clicking the provided link.
  6. Best Functional Significance

    The minimum significance for the structure predictions.
  7. Description

    The user specified information for the structure predictions.

Result page of "Generate & Rank Predictions"

The generated structure predictions by the specified prediction tools and their rankings are summarized in this page.

  1. Job_ID

    The web service Job_ID of.
  2. Job Description

    The sequence information provided in the header of the given .fasta file.
  3. Parameters

    The user-specified algorithm parameters.
  4. The Meta-stable Structure

    The suggested most native-like candidate structure form the given conformation predictions.
    • (a) Structure: The meta-stable structure can be visualized or downloaded by clicking the provided link.
    • (b) Best Functional Significance: The minimum significance in the functional interpretability metrics.
    • (c) Significance metrics: The functionally interpretability test results of the meta-stable structure.
  5. Structure

    The predicted structure can be visualized or downloaded by clicking the provided link.
  6. Best Functional Significance

    The minimum significance for the structure predictions.
  7. Generating tool

    The prediction tool from which the sub-optimal structure was adopted.

Result page of Infer Interpretability

Infer the functional interpretability for the given structure.

  1. Job_ID

    The web service Job_ID.
  2. Job Description

    The sequence information provided in the header of the dot bracket file.
  3. Parameters

    The user-specified algorithm parameters in identifying the functionally interpretable structure.
  4. The Structur Functional Interpretability

    • (a) Structure: The meta-stable structure can be visualized or downloaded by clicking the provided link.
    • (b) Best Functional Significance: The minimum significance in the functional interpretability metrics.
    • (c) Significance metrics: The functionally interpretability test results of the meta-stable structure.