We have developed some softwares for bioinformatics analysis. You may need to register for the use of some of them.



A resource of cell-specific transcriptional information for human microRNAs


An integrated platform providing high quality gene interactions data in human mitochondrion and useful tools to analysis interaction network.


Tissue Specific Transcriptional Regulatory Network Motif Database


A comprehensive microRNA target repository of bidirectional interspecies regulation between viruses and human.



Cepa utilizes pathawy topology information to find significant pathways. It highlights improtant genes in the pathway from different aspect that realtes to biological functions.


SiGPAT is a useful tool based on gene set analysis for microarray data. It can find significant expression pattern of gene sets by pri-defined biological knowledge and can help users to determine whether genes are singular up regulated or down regulated or with both up and down regulation under certain biological circumstances.


MiRmat is a software designed to predict mature microRNA from pri-microRNA. This tool can be divided into two parts, one is for predicting Drosha processing site, which is based on energy distribution pattern along primary microRNA's secondary structure; the other is for predicting Dicer processing site, which is based on precursor microRNA's structure feature.


MACO is a Position Frequency Matrix(PFM) comparing application that implements a gap-allowed alignment algorithm. You may compare your PFM with those collected in our dataset.


Flexible Motif Search (FMS) is a transcription factor binding site prediction tool. It reads position frequency matrices(PFMs)/consensus sequences and DNA sequences in FASTA/Genbank as the input. FMS searhes the input motifs along the DNA sequences and outputs plot, position of matching sites and clusters of these sites. Motifs which are related to the input motifs can also be retrieved from the MACO interface.


PMSearch (Poly Matrix Search) is a tool that utilizes Position Weight Matrices to search for putative Transcription Factor Binding Sites. PMSearch takes Position Frequency Matrices (PFMs) and DNA sequences to initiate a prediction task. The user may upload motifs/matrices (Position Frequency Matrices, PFM or Position Weight Matrices, PWM))or retrieve PFMs from our local dataset as input. We currently have 507 PFMs downloaded from Transfac Public Database 7.0 and JASPAR. Besides PFMs, the user may add multiple sequences in FASTA or Genbank format. PMSearch outputs a plot, a table of location, score and motif of each high scoring site and clusters of these sites. PFMs which are relative to each input PFM could be retrieved respectively to assist promoter analysis.

MiRNA Spotter

This program is designed to predict the miRNA precursor with a new secondary structure prediction algorithm that is special for the stem-loop structure for the miRNA precursor. We do not limit the miRNA precursor to pri-miRNA or pre-miRNA as the cutting site of Drosha is not clear enough and the length limitation of pri-miRNA is also under research.


A tool for identifying Over-represented and Conserved Word