{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T09:23:27Z","timestamp":1768555407418,"version":"3.49.0"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>mRNA polyadenylation is responsible for the 3\u2032 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.<\/jats:p>\n               <jats:p>Contact: \u00a0btian@umdnj.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl394","type":"journal-article","created":{"date-parts":[[2006,7,27]],"date-time":"2006-07-27T00:58:50Z","timestamp":1153961930000},"page":"2320-2325","source":"Crossref","is-referenced-by-count":104,"title":["Prediction of mRNA polyadenylation sites by support vector machine"],"prefix":"10.1093","volume":"22","author":[{"given":"Yiming","family":"Cheng","sequence":"first","affiliation":[{"name":"Department of Mathematical Sciences, New Jersey Institute of Technology 1 \u00a0 1 \u00a0 \u00a0 Newark, NJ 07102, USA"},{"name":"Department of Biochemistry and Molecular Biology, New Jersey Medical School 2 \u00a0 2 \u00a0 \u00a0 University of Medicine and Dentistry of New Jersey, Newark, NJ 07101, USA"}]},{"given":"Robert M.","family":"Miura","sequence":"additional","affiliation":[{"name":"Department of Mathematical Sciences, New Jersey Institute of Technology 1 \u00a0 1 \u00a0 \u00a0 Newark, NJ 07102, USA"}]},{"given":"Bin","family":"Tian","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, New Jersey Medical School 2 \u00a0 2 \u00a0 \u00a0 University of Medicine and Dentistry of New Jersey, Newark, NJ 07101, USA"}]}],"member":"286","published-online":{"date-parts":[[2006,7,26]]},"reference":[{"key":"2023012409233843100_b1","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1007\/s002510100358","article-title":"A rare polyadenylation signal mutation of the FOXP3 gene (AAUAAA\u2192AAUGAA) leads to the IPEX syndrome","volume":"53","author":"Bennett","year":"2001","journal-title":"Immunogenetics"},{"key":"2023012409233843100_b2","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/j.ceb.2005.04.003","article-title":"Connections between mRNA 3\u2032 end processing and transcription termination","volume":"17","author":"Buratowski","year":"2005","journal-title":"Curr. 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