Prediction of mRNA polyadenylation sites by support vector machine

Document Type

Article

Publication Date

1-1-2006

Abstract

mRNA polyadenylation is responsible for the 3′ end formation of most mRNAs in eukaryotic cells and is linked to termination of transcription. Prediction of mRNA polyadenylation sites [poly(A) sites] can help identify genes, define gene boundaries, and elucidate regulatory mechanisms. Current methods for poly(A) site prediction achieve moderate sensitivity and specificity. Here, we present a method using support vector machine for poly(A) site prediction. Using 15 cis -regulatory elements that are over-represented in various regions surrounding poly(A) sites, this method achieves higher sensitivity and similar specificity when compared with polyadq, a common tool for poly(A) site prediction. In addition, we found that while the polyadenylation signal AAUAAA and U-rich elements are primary determinants for poly(A) site prediction, other elements contribute to both sensitivity and specificity of the prediction, indicating a combinatorial mechanism involving multiple elements when choosing poly(A) sites in human cells. © 2006 Oxford University Press.

Identifier

33749997848 (Scopus)

Publication Title

Bioinformatics

External Full Text Location

https://doi.org/10.1093/bioinformatics/btl394

e-ISSN

13674811

ISSN

13674803

PubMed ID

16870936

First Page

2320

Last Page

2325

Issue

19

Volume

22

Fund Ref

Nanjing Institute of Technology

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