README.md

LncReader

Table of Contents

• Test Dataset Descriptions
  • Mouse coding lncRNA Test Dataset
  • Fruit Fly coding lncRNA Test Dataset
  • Joint analysis of RNAseq-Ribosome-MS Test Dataset
• How-to-run-LncReader?
• What's-the-aim-of-LncReader?

Test Dataset Descriptions (stored in this repository)

1. Mouse coding lncRNA Test Dataset

File path: LncReader/test/Mouse_coding_lncRNA_test_dataset.fa

This test dataset contains data specifically for mouse coding long non-coding RNAs (lncRNAs).

2. Fruit Fly coding lncRNA Test Dataset

File path: LncReader/test/Drosophila_coding_lncRNA_test_dataset.fa

Similarly, this test dataset includes data specifically for fruit fly coding long non-coding RNAs (lncRNAs).

3. Joint analysis of RNAseq-Ribosome-MS Test Dataset

File path: LncReader/test/RNA-Ribosome-MS.xlsx

This test dataset includes data specifically for leukaemia cell lines.

How to run LncReader

1. Input File

Prepare your input file, which should be in fasta format. For example, the file name could be input.fasta.

2. Output File

Define a name for your output file, which will be used to store the results processed by the script. For example, you might name your output file output.txt.

3. Download this repository and open the Command Line Interface

Open a terminal (Linux or MacOS) or Command Prompt/PowerShell (Windows).

4. Navigate to the Directory Containing the Script

Use the cd command to navigate to the directory where your script is saved. For example:

cd LncReader/myPackage/

5. Run the Script

Use the following command to run the script, replacing <input_file> and <output_file> with your actual file paths.

python run_lncReader.py <input_file> <output_file>

For example:

python run_lncReader.py ../test/Drosophila_coding_lncRNA_test_dataset.fa output.txt

6. Example Output

The output file will contain the identifier of each sequence, the calculated score (the probility of dual functional lncRNA), and the sequence itself. For example:

>Sequence1  0.4789213  GATTACAGATTACA...
>Sequence2  0.5293812  GTCAGTCAGTCAGT...
 ...

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What's the aim of LncReader

We aim to explore whether LncReader provides a sophisticated and practical tool to identify dual functional lncRNAs and explore potentially lncRNA-encoded micropeptides, which might assist dissection the key roles of dual functional lncRNAs in either physiology or pathology conditions.

The research of LncReader is online. Please cite us with LncReader: identification of dual functional long noncoding RNAs using a multi-head self-attention mechanism