Kegg-Hidden-Loop-Search

Hidden regulatory relationship for a loop on gene regulation networks
are not completely revealed for most of biological pathway database.
Hence, we hope to write a program that can find the hidden loops back.

This project is an example to use the library, Feedback_Loop_Search.jar, on searching kegg hidden loop.
In repository, you can find many main files, representing each stage in a complete searching experiment.
You can read ExecutionMain.java to know more about the process of the experiment.
The library applies kegg database as the main resource for searching hidden loops.
Hoping this can help you using library to write your own program, according to your needs.

If wanting to search hidden loops on kegg database instantly, you can find archive file below.
If interested in the methodology of searching hidden loops on kegg database, you can find doc here.

If there is any problem, you can send email to me, or leave an anonymous message here.
If using the anonymous system, you should tell me which repository you are talking about.

Thanks a lot! ☺️

Development Environment

• Eclipse
• Java Development Kit
• under windows 10 32-bit OS

KGI

The searching is based on KGI, an integrated data structure parsed from kegg database in specific species.

• Find the KGI file immediately under res directory on this repository
  • KEGG Orthology
    1. Org Code: ko
    2. find the KGI file here
    3. retrieved from KEGG on 2017/05/07
    4. place Kgml_Info.ki in specific directory: ~/Database/Kgml_Information/ko/
  • Danio rerio (zebrafish)
    1. Org Code: dre
    2. find the KGI file here
    3. retrieved from KEGG on 2017/06/09
    4. place Kgml_Info.ki in specific directory: ~/Database/Kgml_Information/dre/
  • Homo sapiens (human)
    1. Org Code: hsa
    2. find the KGI file here
    3. retrieved from KEGG on 2017/06/09
    4. place Kgml_Info.ki in specific directory: ~/Database/Kgml_Information/hsa/

Archive File

• Here you can find the archive file for this project
• Here you can find what is inside the archive file
  • Here you can find the user guide

Library Document

Here you can find the java document for Feedback_Loop_Search.jar.