Predictive modeling of plant messenger RNA polyadenylation sites

doi:10.1186/1471-2105-8-43

BMC Bioinformatics

Volume 8

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Research article

Predictive modeling of plant messenger RNA polyadenylation sites

Guoli Ji¹ , Jianti Zheng¹ , Yingjia Shen² , Xiaohui Wu¹ , Ronghan Jiang¹ , Yun Lin¹ , Johnny C Loke²^,4 , Kimberly M Davis² , Greg J Reese³ and Qingshun Quinn Li²

¹Department of Automation, Xiamen University, Xiamen, Fujian, 361005, P. R. China

²Department of Botany, Miami University, Oxford, OH 45056, USA

³Research Computing Group, IT Services, Miami University, Oxford, OH 45056, USA

⁴Current address: Department of Medicine, Division of Liver Diseases, Mount Sinai Medical Center, 1425 Madison Avenue, RM 1176, New York, NY 10029, USA

author email corresponding author email

BMC Bioinformatics 2007, 8:43doi:10.1186/1471-2105-8-43


Published:	7 February 2007

Additional files

Additional File 1:

Forward-backward Algorithm of GHMM Used in PASS. Details on how GHMM was implemented in the algorithm, including parameter settings and mathematical formulas.

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Additional File 2:

The distribution of nucleotides in the 20 nt region around poly(A) sites. Fraction of each of the four nucleotides around poly(A) sites.

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Additional File 3:

Analysis of the lengths of signal elements in FUE, NUE, CE-L and CE-R. Data showing the reason why the length of nucleotide sequences of each signal element was chosen.

Format: PDF Size: 138KB Download file

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Additional File 4:

Frequency of eight nucleotides patterns with high counts in FUE. Ranked list of the counts of the top 50 patterns found in FUE.

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Additional File 5:

Statistical features of the background. Numeric data for setting background parameter.

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