Jinzer Documentation

Description

Create gene set based on transcription factor binding sites ranked by Jindex.

Release

Source code 1.0.0 08/18/2024

Binary Windows, Mac OS, Linux

Install

Go the source folder and run gcc Jinzer-1.0.c cdflib.c -std=c11 -static -o Jinzer command, a binary named flaver will produced in the folder.

Under windows OS try gcc Jinzer-1.0.c cdflib.c -std=c11 -static -o Jinzer.exe instead.

Requirement

Minimum 2GB memory, if you install from the source code, the gcc complier is also required.

Usage

Jinzer -m motif -i seq [-s seed] [-n rand_n] [-r score] -o output

Options

-m PWMs for transcription factors

-i putative promoter sequence in fasta format

-n sampling n for test run

-r threshold for Jindex

-o output, output file name

Example Data

motif file: Motiff_Jaspar-2022+HOCO-v11.txt

promoter sequence: Human_promoter.txt

results: Human_jinzer_output.txt

Example

An example run should like: ./Jinzer -m Motiff_Jaspar-2022+HOCO-v11.txt -i Human_promoter.txt -r 1.0 -o Human_jinzer_output.txt

This command took two input files: Motiff_Jaspar-2022+HOCO-v11.txt, Human_promoter.txt. After finished run it will produce an output file nameded Human_jinzer_output.txt.

References

Tinghua Huang, Binyu Wang, Faqiang Luo, Jianwu Wang, Guopin Liu, Min Yao. Correlating gene expression levels with transcription factor binding sites facilitates identification of key transcription factors from transcriptional data.

Contact

Dr. Tinghua Huang, thua45@126.com

Dr. Min Yao, minyao@yangtzeu.edu.cn