CNEFinder: finding conserved non-coding elements in genomes
CNEFinder: finding conserved non-coding elements in genomes
复制标题
CNEFinder：寻找基因组中保守的非编码元件
DOI：
--
复制
发表时间：
2018
期刊：
影响因子：
--
通讯作者：
D. Polychronopoulos
中科院分区：
文献类型：
--
作者：
Lorraine A. K. Ayad;S. Pissis;D. Polychronopoulos
保守的非编码元件（CNE）代表了一类神秘的基因组元件，尽管在进化过程中非常保守，但不编码蛋白质。它们的功能在很大程度上仍然未知。因此，需要系统地研究它们在基因组中的作用。朝着这个方向，在广泛的生物体中识别CNE集是重要的第一步。目前，在文献中还没有发表用于系统地鉴定基因组中的CNE的工具。结果我们通过展示Symbol填补了这一空白; Symbol是一种用于识别两个给定DNA序列之间的CNE的工具，具有用户定义的标准。实验结果表明该工具能够准确、高效地识别CNEs。Symbol基于k‐mer技术来计算最大精确匹配。因此，该工具不需要或计算全基因组比对或索引，例如后缀数组或Burrows惠勒变换（BWT），这使得它可以灵活地在大范围内使用。符号.无标题。可用性和实施GNU GPL条款下的自由软件（https：//github.com/lorrainea/CNEASYPE）。
Motivation Conserved non‐coding elements (CNEs) represent an enigmatic class of genomic elements which, despite being extremely conserved across evolution, do not encode for proteins. Their functions are still largely unknown. Thus, there exists a need to systematically investigate their roles in genomes. Towards this direction, identifying sets of CNEs in a wide range of organisms is an important first step. Currently, there are no tools published in the literature for systematically identifying CNEs in genomes. Results We fill this gap by presenting Symbol; a tool for identifying CNEs between two given DNA sequences with user‐defined criteria. The results presented here show the tool's ability of identifying CNEs accurately and efficiently. Symbol is based on a k‐mer technique for computing maximal exact matches. The tool thus does not require or compute whole‐genome alignments or indexes, such as the suffix array or the Burrows Wheeler Transform (BWT), which makes it flexible to use on a wide scale. Symbol. No caption available. Availability and implementation Free software under the terms of the GNU GPL (https://github.com/lorrainea/CNEFinder).
影响因子：
7
作者：
Schwartz, S;Kent, WJ;Miller, W
通讯作者：
Miller, W
影响因子：
7
作者：
Blanchette, M;Kent, WJ;Miller, W
通讯作者：
Miller, W