Identification of possible differences in coding and non-coding fragments of DNA sequences by using the method of the Recurrence Quantification Analysis
Starting with the results of Li et al. in 1992 there is valuable interest in finding long range correlations in dna sequences since it raises questions about the role of introns and intron-containing genes. In the present paper we studied two sequences. We applied the method of the recurrence quantification analysis (rqa) that was introduced by Zbilut and Webber in 1994. The significant result that we have here is that both Lmax and Laminarity exhibit very large values in non coding respect to coding sequences. Therefore we suggest that there the claimed higher long range correlations of introns respect to exons from many authors may be explained here in reason of such found higher values of Lmax and of Laminarity.
Emerging Challenges in Molecular Paleontology: Misapplication of Environmental DNA Fragments and Misconception of Deamination as a Key Criterion for In Situ DNA Identification
Linking de novo assembly results with long DNA reads by dnaasm-link application
目前，与下一代测序技术相比，允许获得更长的DNA读数的第三代测序技术正变得越来越流行。有许多可能性可以将下一代和第三代测序的数据结合起来。在此，我们提出了一个新的应用程序称为dnaasm-link连接重叠群，\textit{de novo}组装的第二代测序数据的结果，与长的DNA读取。我们的工具包括一个集成模块，用于使用适当长的DNA读段的合适片段来填补空白，这提高了所得DNA序列的一致性。该特征非常重要，特别是对于复杂的DNA区域，如本文所述。最后，我们的实现在速度和内存要求方面优于其他最先进的工具，这可能使所呈现的应用程序能够用于具有大基因组的生物体，这在现有应用程序中是不可能的。所提出的应用具有许多优点，如（i）显著的存储器优化和计算时间的减少（ii）通过指定的长DNA读段的适当片段填充缺口（iii）减少现有基因组草图中跨越和未跨越缺口的数量。该应用程序在GNU Library或Lesser General Public License version 3.0（LGPLv3）下免费提供给所有用户。演示应用程序、Docker镜像和源代码可在www.example.com上获得。
AntigenLM: Structure-Aware DNA Language Modeling for Influenza
Computer Network Information Center, Chinese Academy of Sciences（中国科学院计算机网络信息中心）；Beijing Institute of Genomics, Chinese Academy of Sciences（中国科学院北京基因组研究所）；China National Center for Bioinformation（中国生物信息学国家中心）；University of Chinese Academy of Sciences（中国科学院大学）
