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This article is part of the supplement: Selected articles from the Eleventh Asia Pacific Bioinformatics Conference (APBC 2013): Bioinformatics

Open Access Proceedings

A multispecies polyadenylation site model

Eric S Ho1*, Samuel I Gunderson2 and Siobain Duffy3

Author Affiliations

1 Department of Molecular Genetics, Microbiology and Immunology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA

2 Department of Molecular Biology and Biochemistry, Rutgers University, New Brunswick, New Jersey, USA

3 Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ, USA

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BMC Bioinformatics 2013, 14(Suppl 2):S9  doi:10.1186/1471-2105-14-S2-S9

Published: 21 January 2013

Additional files

Additional file 1:

Table S1: Existing poly(A) sites methods. Figure S1: Feature identification by Principal Component Analysis (PCA). Figure S2: PCA of real poly(A) sequences. The canonical poly(A) signal is a misguiding feature. Figure S3: ROC of logistic method. Table S2: False positive rate (in percentage) committed by different methods in handling CDS gene sequences. Table S3: Relative contribution of individual features. Figure S4: Predictions of five hundred 2,000-nt poly(A) sites by sliding a 600-nt sliding window from left to right. Figure S5. Correlation between phylogenetic distance and reciprocal sensitivity (rSn) between seven species: human, mouse, chicken, c.elegans, rice, Arabidopsis, and tomato.

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