Research article
Predictive modeling of plant messenger RNA polyadenylation sites
1 Department of Automation, Xiamen University, Xiamen, Fujian, 361005, P. R. China
2 Department of Botany, Miami University, Oxford, OH 45056, USA
3 Research Computing Group, IT Services, Miami University, Oxford, OH 45056, USA
4 Current address: Department of Medicine, Division of Liver Diseases, Mount Sinai Medical Center, 1425 Madison Avenue, RM 1176, New York, NY 10029, USA
BMC Bioinformatics 2007, 8:43 doi:10.1186/1471-2105-8-43
Published: 7 February 2007Additional 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.
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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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