DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences

Liu HQ; Han H; Li JY; Wong LS

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DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences

机译：DNAFSMiner：基于网络的软件工具箱，可识别DNA序列中的两种类型的功能位点

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DNAFSMiner (DNA Functional Sites Miner) is a web-based software toolbox to recognize functional sites in nucleic acid sequences. Currently in this toolbox, we provide two software: TIS Miner and Poly(A) Signal Miner. The TIS Miner can be used to predict translation initiation sites in vertebrate DNA/mRNA/cDNA sequences, and the Poly(A) Signal Miner can be used to predict polyadenylation [poly(A)] signals in human DNA sequences. The prediction results are better than those by literature methods on two benchmark applications. This good performance is mainly attributable to our unique learning method. DNAFSMiner is available free of charge for academic and non-profit organizations.

机译：DNAFSMiner（DNA功能位点挖掘器）是一个基于Web的软件工具箱，用于识别核酸序列中的功能位点。当前，在此工具箱中，我们提供两个软件：TIS Miner和Poly（A）Signal Miner。 TIS Miner可用于预测脊椎动物DNA / mRNA / cDNA序列中的翻译起始位点，而Poly（A）Signal Miner可用于预测人类DNA序列中的聚腺苷酸化[poly（A）]信号。在两个基准应用上，预测结果优于文献方法。这种良好的表现主要归功于我们独特的学习方法。学术和非营利组织均可免费使用DNAFSMiner。

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来源
《Bioinformatics》 |2005年第5期|p. 671-673|共3页
作者
Liu HQ; Han H; Li JY; Wong LS;
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作者单位

Inst Infocomm Res, Singapore 119613, Singapore;

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收录信息美国《科学引文索引》(SCI);美国《化学文摘》(CA);
原文格式 PDF
正文语种 eng
中图分类生物科学;
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专利

1. DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences [J] . Liu HQ, Han H, Li JY, Bioinformatics . 2005,第5期

机译：DNAFSMiner：基于网络的软件工具箱，可识别DNA序列中的两种类型的功能位点
2. BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences [J] . Liangjiang Wang, Susan J. Brown Nucleic acids research . 2006,第suppla2期

机译：BindN：基于网络的工具，可有效预测氨基酸序列中的DNA和RNA结合位点
3. Sequence preference in DNA binding: de novo designed helix-turn-helix metallopeptides recognize a family of DNA target sites [J] . Wong-Deyrup SW, Kim Y, Franklin SJ Journal of biological inorganic chemistry: JBIC: a publication of the Society of Biological Inorganic Chemistry . 2006,第1期

机译：DNA结合中的序列偏好：从头设计的螺旋-转-螺旋金属肽识别一个DNA靶位点家族
4. Application of symmetry patterns to recognition of functional sites and phylogenetic analysis of DNA sequences [C] . Akberova, N.I., Yu, Intelligence and Systems, 1998. Proceedings., IEEE International Joint Symposia on . 1998

机译：对称模式在功能位点识别和DNA序列系统发育分析中的应用
5. Methylation and chromatin conformation of adenovirus type 12 DNA sequences in transformed cells. [D] . Redfield, Rosemary Jeanne. 1980

机译：转化细胞中12型腺病毒DNA序列的甲基化和染色质构象。
6. DNA Data Visualization (DDV): Software for Generating Web-Based Interfaces Supporting Navigation and Analysis of DNA Sequence Data of Entire Genomes [O] . Tomasz Neugebauer, Eric Bordeleau, Vincent Burrus, 2010

机译：DNA数据可视化（DDV）：用于生成基于Web的界面的软件，支持导航和分析整个基因组的DNA序列数据
7. : "This paper deals with the functionality of the flaked stone assemblages from several Neolithic sites of the NE of the Iberian Peninsula. The chronological framework ranges from the mid-6th to the mid-4th millennium cal. BCE, which corresponds to the Early and Middle Neolithic. This long period ranges from the arrival of the first farming communities in the Iberian Peninsula, around 5600-5500 cal. BCE, to 3600-3500 cal. BCE, two millennia later, when Neolithic communities had stably occupied most of the available territory, from the mountainous areas of the Pyrenees to the coastal areas of the Mediterranean.In this context, the NE of the Iberian Peninsula is one of the areas where a major number of use-wear analyses have been carried out, especially for what concerns the Neolithic period. This is mainly due to the interest shown by the directors of the excavations and by the Spanish use-wear specialists as well; both participated and cooperated in order to enlarge the number of contexts studied, making the NE of the Iberian Peninsula one of the areas of Europe with the largest number of ‘functional studies’. As a result, today we have a reliable picture of the type of lithic tools used by the first farming groups, how they were used, and which needs they were satisfying.The methodology employed for this type of analysis is today broadly shared by most use-wear specialists. A stereoscopic microscope is used together with a reflected-light microscope for the analysis of the archaeological specimens. Afterwards, the observed use-wear traces are compared with the traces from experimental tools. This study primarily made use of the tools preserved at the ‘Traceoteque’ of the Institución Milà y Fontanals of the CSIC of Barcelona.This paper presents the results obtained for the different types of analysed sites and the relative lithic assemblages. In this way, tools from different contexts are compared: open-air sites, caves and rock-shelters, pit-sites, burials, and mining sites. Such a diversity of contexts allowed for the exploration of the existence of recurrences and differences in the functionality of the lithic tools from one site to another. The results obtained have also provided information on some aspects related to the economic processes carried out at the different sites, caves, rock-shelters and open-air contexts. It has been possible to gain fresh data on the types of tasks carried out and their relative importance for each site, their relation with the geographical and environmental context and the natural resources available there. In addition, analysing tools recovered from burials – mainly individual inhumations – provided information on the relationships between the buried individuals and the working tools, in particular exploring the relationships between sex and age patterns and the types of tools deposited as goods.In conclusion, use-wear analysis allowed for the exploration of a variety of issues; from technical aspects related to the production and management of the lithic resources to social aspects related to the subsistence activities and the individuals that carried them out." [O] . Gibaja Bao, Juan Francisco, Mazzucco, Niccolo 2015

机译：：“本文研究了伊比利亚半岛东北部几个新石器时代遗址的片状石材组合的功能。时间框架从公元前6世纪中叶到4世纪中叶，分别对应于早期和早期。新石器时代中期，这段时间的长短是从伊比利亚半岛的第一个农业社区到来，大约在公元前5600-5500 cal，到了两千年后的3600-3500 BCE，当时新石器时代的社区稳定地占据了大部分可用土地。从比利牛斯山脉山区到地中海沿岸地区。在这种情况下，伊比利亚半岛东北部是进行过大量使用磨损分析的地区之一，尤其是在关注方面新石器时代，这主要是由于发掘负责人和西班牙使用服装专家表现出的浓厚兴趣；他们参与和合作以扩大孔蒂的数量xts进行了研究，使伊比利亚半岛的NE成为“功能研究”数量最多的欧洲地区之一。结果，今天我们可以可靠地了解第一批耕作小组使用的石器工具的类型，使用方法以及它们满足的需求。今天，大多数使用方法广泛共享用于这种类型的分析的方法穿专家。立体显微镜与反射光显微镜一起用于分析考古样本。然后，将观察到的使用磨损痕迹与实验工具的痕迹进行比较。这项研究主要利用了巴塞罗那CSIC的米拉·丰塔纳尔研究所的“ Traceoteque”中保存的工具。本文介绍了针对不同类型的分析地点和相对石器组合所获得的结果。通过这种方式，可以比较来自不同环境的工具：露天场所，洞穴和岩石避难所，露天场所，埋葬场所和采矿场所。如此多样的上下文允许探索重复性的存在以及从一个站点到另一个站点的石器工具的功能差异。所获得的结果还提供了与在不同地点，洞穴，避难所和露天环境中进行的经济过程有关的某些方面的信息。可以获得有关所执行任务的类型及其对每个站点的相对重要性，它们与地理和环境环境以及那里可用自然资源的关系的新数据。此外，对从墓葬中回收的工具（主要是个人遗体）进行分析，可提供有关被掩埋的个体与工作工具之间关系的信息，尤其是探索性别与年龄模式之间的关系以及作为商品存放的工具的类型。磨损分析允许探索各种问题；从与石器资源的生产和管理有关的技术方面到与自给活动及其实施者有关的社会方面。”

DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences

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