Download Datasets and Programs Described in Our Publications:

(Click on the links to download datasets, software or publications)

1. The following files are associated with this publication:

Johnny C . Loke, Eric A. Stahlberg, David G. Strenski, Brian Haas, Paul Chris Wood, and Qingshun Quinn Li. 2005. Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures. Plant Physiology, 138: 1457-1468.

a. 8K dataset: over 8000 Arabidopsis 3'-UTRs (300 nt) plus downstream sequences (100 nt)

b. 16K dataset: over 16,000 Arabidopsis 3'-UTRs (300 nt) plus downstream sequences (100 nt)

c. Source code for SignalSleuth2 (an updated version of original SignalSleuth)

2. The following file is associated with this publication:

Guoli Ji, Jianti Zheng, Yingjia Shen, Xiaohui Wu, Ronghan Jiang, Yun Lin, Johnny C. Loke, Kimberly M. Davis, Greg J. Reese and Q. Quinn Li. 2007. Predictive modeling of plant messenger RNA polyadenylation sites. BMC Bioinformatics, 8:43 (doi:10.1186/1471-2105-8-43).

a. PASS1.0 Program

3. The following file is associated with this paper:

Yingjia Shen, Guoli Ji, Brian J. Haas, Xiaohui Wu, Jianti Zheng, Greg J. Reese and Qingshun Quinn Li. 2008. Genome level analysis of rice mRNA 3’-end processing signals and alternative polyadenylation. Nucleic Acids Research, 36:3150-3161

a. Rice 55K poly(A) site dataset

b. PASS-Rice program package

4. The following file is associated with this paper:

Yingjia Shen, Yuansheng Liu, Lin Liu, Chun Liang and Qingshun Q. Li. Unique Features of Nuclear mRNA Poly(A) Signals and Alternative Polyadenylation in Chlamydomonas reinhardtii. Genetics, 179:167-176.

a. Chlamydomonas 17K poly(A) site dataset

5. The following file is associated with this paper:

Guoli Ji, Xiaohui Wu, Yingjia Shen, Jiangyin Huang and Q. Quinn Li. 2010. Classification-Based Prediction Models of Messenger RNA Polyadenylation Sites. Journal of Theoretical Biology, 265:287-296.

a. PAC software package for testing and demonstration purposes

6. The following file is associated with this paper:

Zhixin Zhao, Xiaohui Wu, Praveen Kumar Raj Kumar, Min Dong, Guoli Ji, Q. Quinn Li and Chun Liang. 2014. Bioinformatics analysis of alternative polyadenylation in green alga Chlamydomonas reinhardtii using transcriptome sequences from three different sequencing platforms. doi: 10.1534/g3.114.010249 Genes Genomics Genetics (G3), 265:287-296.

a. Poly(A) datasets

7. The following files is associated with this paper:

Denghui Xing, Q. Quinn Li. 2014. RADPRE: a computational program for identification of differential mRNA processing including alternative polyadenylation. In Polyadenylation in Plants. Editors: A.G. Hunt and Q.Q.Li. Series: Methods in Molecular Biology; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

a. Software package for Mac users (160 MB)

b. Software package for PC users (160 MB)

8. The following file is associated with this paper:

Xiaohui Wu, Guoli Ji, Q. Quinn Li. 2014. Computational analysis of plant polyadenylation signals. In Polyadenylation in Plants. Editors: A.G. Hunt and Q.Q.Li. Series: Methods in Molecular Biology; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

a. Signal Sleuth-2 software package

9. The following file is associated with this paper:

Xiaohui Wu, Guoli Ji, Q. Quinn Li. 2014. Prediction of plant polyadenylation sites. In Polyadenylation in Plants. Editors: A.G. Hunt and Q.Q.Li. Series: Methods in Molecular Biology; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

a. Poly(A) Site Sleuth (PASS) software package

b. Poly(A) Classifier (PAC) software package

10. The following file is associated with this paper:

Xiaohui Wu, Guoli Ji, Q. Quinn Li. 2014. PAT-seq data processing to extract poly(A) sites and their analysis. In Polyadenylation in Plants. Editors: A.G. Hunt and Q.Q.Li. Series: Methods in Molecular Biology; Series Editor: John Walker. Humana Press, Springer Publishing Group, USA.

a. Poly(A) site extraction from PAT-seq dataset software package