Software

GleClubs

GLECLUBS is an algorithm for predicting cis-regulatory binding sites in prokaryotes, which was described in the following papers: 

  • Shaoqiang Zhang, MinLi Xu, Shan Li, and Zhengchang Su. Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes. Nucleic Acids Research, 2009. doi:10.1093/nar/gkp248. (pdf)
  • Zhang S, Li S, Pham PT, Su Z. Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes. BMC Bioinformatics. 2010;11:397. PMCID: 2920276. (pdf)

TFBS PFM database search using PFV algorithm

TFBS PFM database search is web interface which demonstrate the effectiveness of our PFV algorithm for PFM searching and retrieval.

  • Xu M, Su Z. A novel alignment-free method for comparing transcription factor binding site motifs. PLoS One. 2010;5(1):e8797. (pdf)

MotifClick

MotifClick is a motif-finding tools

  • Shaoqiang Zhang, Shan Li, Meng Niu, Phuc Pham and Zhengchang Su. MotifClick: prediction of cis-regulatory binding sites via merging cliques. BMC Bioinformatics 2011, 12:238 (pdf)

TruHMM

The software and code will be released upon the publication of the the paper.

TruHMM assembles transcription unit/operons in prokaryotes using RNA-seq short reads

  • Shan Li, Xia Dong and Zhengchang Su. Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genomics. 2013 Jul 30;14:520. (pdf)

SNN-Cliq

SNN-Cliq is a method for partitioning individuall cells into grooups of the same type using single-cell transcriptome data. 

  • Chen Xu and Zhengchang Su. Identification of cell types from single-cell transcriptome using a novel clustering method. Bioinformatics 2015 (btv088)