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Bioinformatics. 2013 Jan 1;29(1):117-8. doi: 10.1093/bioinformatics/bts638. Epub 2012 Oct 30.
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Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels.鉴定拟南芥、杨树、葡萄和水稻中的共享单拷贝核基因及其在不同分类水平上的系统发育应用。
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Global sequence features based translation initiation site prediction in human genomic sequences.基于全局序列特征的人类基因组序列翻译起始位点预测
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Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA.全聚腺苷酸：一种准确识别人类基因组DNA中聚腺苷酸信号的方法和工具。
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本文引用的文献

1
MetWAMer: eukaryotic translation initiation site prediction.MetWAMer：真核生物翻译起始位点预测
BMC Bioinformatics. 2008 Sep 18;9:381. doi: 10.1186/1471-2105-9-381.
2
Prediction of translation initiation sites in human mRNA sequences with AUG start codon in weak Kozak context: A neural network approach.在弱科扎克环境下具有AUG起始密码子的人类mRNA序列中翻译起始位点的预测：一种神经网络方法。
Biochem Biophys Res Commun. 2008 May 16;369(4):1166-8. doi: 10.1016/j.bbrc.2008.03.008. Epub 2008 Mar 13.
3
Translation initiation site prediction on a genomic scale: beauty in simplicity.基因组规模上的翻译起始位点预测：简约之美。
Bioinformatics. 2007 Jul 1;23(13):i418-23. doi: 10.1093/bioinformatics/btm177.
4
Markov encoding for detecting signals in genomic sequences.用于检测基因组序列中信号的马尔可夫编码
IEEE/ACM Trans Comput Biol Bioinform. 2005 Apr-Jun;2(2):131-42. doi: 10.1109/TCBB.2005.27.
5
Computational approaches to gene prediction.基因预测的计算方法。
J Microbiol. 2006 Apr;44(2):137-44.
6
Feature selection for the prediction of translation initiation sites.用于预测翻译起始位点的特征选择
Genomics Proteomics Bioinformatics. 2005 May;3(2):73-83. doi: 10.1016/s1672-0229(05)03012-3.
7
Using amino acid patterns to accurately predict translation initiation sites.利用氨基酸模式准确预测翻译起始位点。
In Silico Biol. 2004;4(3):255-69.
8
Data mining tools for biological sequences.生物序列的数据挖掘工具。
J Bioinform Comput Biol. 2003 Apr;1(1):139-67. doi: 10.1142/s0219720003000216.
9
Starting the protein synthesis machine: eukaryotic translation initiation.启动蛋白质合成机器：真核生物翻译起始
Bioessays. 2003 Dec;25(12):1201-11. doi: 10.1002/bies.10362.
10
Using feature generation and feature selection for accurate prediction of translation initiation sites.利用特征生成和特征选择准确预测翻译起始位点。
Genome Inform. 2002;13:192-200.

龙 TIS 定位器：一种源自拟南芥的植物翻译起始位点预测器。

Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants.

机构信息

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center, Thuwal 23955-6900, Saudi Arabia.

出版信息

Bioinformatics. 2013 Jan 1;29(1):117-8. doi: 10.1093/bioinformatics/bts638. Epub 2012 Oct 30.

DOI:10.1093/bioinformatics/bts638
PMID:23110968
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3530916/
Abstract

SUMMARY

In higher eukaryotes, the identification of translation initiation sites (TISs) has been focused on finding these signals in cDNA or mRNA sequences. Using Arabidopsis thaliana (A.t.) information, we developed a prediction tool for signals within genomic sequences of plants that correspond to TISs. Our tool requires only genome sequence, not expressed sequences. Its sensitivity/specificity is for A.t. (90.75%/92.2%), for Vitis vinifera (66.8%/94.4%) and for Populus trichocarpa (81.6%/94.4%), which suggests that our tool can be used in annotation of different plant genomes. We provide a list of features used in our model. Further study of these features may improve our understanding of mechanisms of the translation initiation.

AVAILABILITY AND IMPLEMENTATION

Our tool is implemented as an artificial neural network. It is available as a web-based tool and, together with the source code, the list of features, and data used for model development, is accessible at http://cbrc.kaust.edu.sa/dts.

摘要

摘要

在高等真核生物中，翻译起始位点（TIS）的鉴定主要集中在寻找 cDNA 或 mRNA 序列中的这些信号。利用拟南芥（A.t.）的信息，我们开发了一种针对植物基因组中与 TIS 相对应的信号的预测工具。我们的工具仅需要基因组序列，而不需要表达序列。它对 A.t.（90.75%/92.2%）、葡萄（Vitis vinifera）（66.8%/94.4%）和杨属（Populus trichocarpa）（81.6%/94.4%）的灵敏度/特异性，这表明我们的工具可用于注释不同的植物基因组。我们提供了模型中使用的特征列表。进一步研究这些特征可能有助于我们理解翻译起始的机制。

可用性和实现

我们的工具是作为人工神经网络实现的。它作为一个基于网络的工具提供，以及源代码、特征列表和用于模型开发的数据可在 http://cbrc.kaust.edu.sa/dts 访问。