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非编码RNA(ncRNA)在全基因组多重比对中的比对准确性如何?

How accurately is ncRNA aligned within whole-genome multiple alignments?

作者信息

Wang Adrienne X, Ruzzo Walter L, Tompa Martin

机构信息

Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195, USA.

出版信息

BMC Bioinformatics. 2007 Oct 26;8:417. doi: 10.1186/1471-2105-8-417.

Abstract

BACKGROUND

Multiple alignment of homologous DNA sequences is of great interest to biologists since it provides a window into evolutionary processes. At present, the accuracy of whole-genome multiple alignments, particularly in noncoding regions, has not been thoroughly evaluated.

RESULTS

We evaluate the alignment accuracy of certain noncoding regions using noncoding RNA alignments from Rfam as a reference. We inspect the MULTIZ 17-vertebrate alignment from the UCSC Genome Browser for all the human sequences in the Rfam seed alignments. In particular, we find 638 instances of chimeric and partial alignments to human noncoding RNA elements, of which at least 225 can be improved by straightforward means. As a byproduct of our procedure, we predict many novel instances of known ncRNA families that are suggested by the alignment.

CONCLUSION

MULTIZ does a fairly accurate job of aligning these genomes in these difficult regions. However, our experiments indicate that better alignments exist in some regions.

摘要

背景

同源DNA序列的多重比对对生物学家来说非常重要,因为它为了解进化过程提供了一个窗口。目前,全基因组多重比对的准确性,尤其是在非编码区域,尚未得到充分评估。

结果

我们以Rfam中的非编码RNA比对为参考,评估某些非编码区域的比对准确性。我们检查了UCSC基因组浏览器中针对Rfam种子比对中所有人类序列的MULTIZ 17种脊椎动物比对。特别是,我们发现了638例与人类非编码RNA元件的嵌合和部分比对情况,其中至少225例可以通过直接方法得到改进。作为我们程序的一个副产品,我们通过比对预测了许多已知ncRNA家族的新实例。

结论

MULTIZ在这些困难区域对这些基因组进行比对的工作做得相当准确。然而,我们的实验表明,在某些区域存在更好的比对。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0009/2206062/1aab4add46e7/1471-2105-8-417-1.jpg

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