酿酒酵母mRNA 3'加工位点的概率预测
Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites.
作者信息
Graber Joel H, McAllister Gregory D, Smith Temple F
机构信息
Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA.
出版信息
Nucleic Acids Res. 2002 Apr 15;30(8):1851-8. doi: 10.1093/nar/30.8.1851.
Abstract
We present a tool for the prediction of mRNA 3'-processing (cleavage and polyadenylation) sites in the yeast Saccharomyces cerevisiae, based on a discrete state-space model or hidden Markov model. Comparison of predicted sites with experimentally verified 3'-processing sites indicates good agreement. All predicted or known yeast genes were analyzed to find probable 3'-processing sites. Known alternative 3'-processing sites, both within the 3'-untranslated region and within the protein coding sequence were successfully identified, leading to the possibility of prediction of previously unknown alternative sites. The lack of an apparent 3'-processing site calls into question the validity of some predicted genes. This is specifically investigated for predicted genes with overlapping coding sequences.
摘要
我们展示了一种基于离散状态空间模型或隐马尔可夫模型来预测酿酒酵母中mRNA 3'加工（切割和聚腺苷酸化）位点的工具。将预测位点与经实验验证的3'加工位点进行比较，结果显示二者吻合度良好。我们对所有预测的或已知的酵母基因进行了分析，以寻找可能的3'加工位点。成功识别出了3'非翻译区内以及蛋白质编码序列内已知的可变3'加工位点，这使得预测此前未知的可变位点成为可能。缺乏明显的3'加工位点对一些预测基因的有效性提出了质疑。我们针对具有重叠编码序列的预测基因对此进行了专门研究。
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本文引用的文献
1
Functional organization of the yeast proteome by systematic analysis of protein complexes.通过对蛋白质复合物的系统分析实现酵母蛋白质组的功能组织
Nature. 2002 Jan 10;415(6868):141-7. doi: 10.1038/415141a.
2
Rna15 interaction with the A-rich yeast polyadenylation signal is an essential step in mRNA 3'-end formation.Rna15与富含A的酵母聚腺苷酸化信号的相互作用是mRNA 3'末端形成的关键步骤。
Mol Cell Biol. 2001 Dec;21(23):8045-55. doi: 10.1128/MCB.21.23.8045-8055.2001.
3
Identifying target sites for cooperatively binding factors.识别协同结合因子的靶位点。
Bioinformatics. 2001 Jul;17(7):608-21. doi: 10.1093/bioinformatics/17.7.608.
4
Identifying the 3'-terminal exon in human DNA.鉴定人类DNA中的3'末端外显子。
Bioinformatics. 2001 Jul;17(7):602-7. doi: 10.1093/bioinformatics/17.7.602.
5
Recognition of polyadenylation sites in yeast pre-mRNAs by cleavage and polyadenylation factor.酵母前体mRNA中聚腺苷酸化位点通过切割和聚腺苷酸化因子的识别
EMBO J. 2001 Jun 15;20(12):3197-209. doi: 10.1093/emboj/20.12.3197.
6
Fip1 regulates the activity of Poly(A) polymerase through multiple interactions.Fip1通过多种相互作用调节聚腺苷酸聚合酶的活性。
Mol Cell Biol. 2001 Mar;21(6):2026-37. doi: 10.1128/MCB.21.6.2026-2037.2001.
7
Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes.变形菌门基因组中转录因子结合位点的系统发育足迹分析
Nucleic Acids Res. 2001 Feb 1;29(3):774-82. doi: 10.1093/nar/29.3.774.
8
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9
An assessment of gene prediction accuracy in large DNA sequences.大型DNA序列中基因预测准确性的评估。
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10
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