[1]杨小雪,张海,贺莎,等.LongMan:一个哺乳类直系同源长链非编码RNA数据库[J].南方医科大学学报,2016,(04):552.
点击复制

LongMan:一个哺乳类直系同源长链非编码RNA数据库()
分享到:

《南方医科大学学报》[ISSN:/CN:]

卷:
期数:
2016年04期
页码:
552
栏目:
出版日期:
2016-04-16

文章信息/Info

Title:
The beta version of LongMan: a large-scale mammalian lncRNA database orthologous to human lncRNAs
作者:
杨小雪张海贺莎林杰朱浩
关键词:
数据库长链非编码RNA同源基因
Keywords:
database long non-coding RNA homologous gene
摘要:
目的计算并预测13 562个GENCODE项目首期鉴定的人类长链非编码RNA在16个哺乳动物的直系同源基因,并建立 数据库LongMan,为长链非编码RNA研究提供重要数据。方法使用RNAfold预测13 562个人类长链非编码RNA每个外显 子的结构;使用Infernal对每个外显子进行基因组搜索,分析其在16个哺乳动物可能的同源外显子;分析每个人类长链非编码 RNA是否有同源基因;分析同源长链非编码RNA中的转座子和剪切信号;构造数据库的搜索引擎和输出界面;实现数据库维护 更新机制。结果LongMan目前收录133 646个直系同源长链非编码RNA;提供序列、比对、转座子和种系特异性插缺(indel) 等信息;提供多条件组合查询;提供显示与下载功能。结论LongMan是首个大规模多种系同源长链非编码RNA数据库,对长 链非编码RNA比较与功能研究具有重要价值。
Abstract:
Objective To predict orthologous sequences of the GENCODE-identified 13 562 human long non-coding RNAs (lncRNA) in 16 mammalian genomes and construct a lncRNA database LongMan for lncRNA studies. Methods The exon structures of a total of 13 562 human lncRNAs were analyzed using RNAfold, and their orthologous sequences were searched against 16 mammalian genomes using Infernal. The potential orthologous genes, transposons and splicing signals of human lncRNAs were predicted to construct a lncRNA database with a updating mechanism. Results and Conclusion The lncRNA database LongMan we constructed, which currently contains 133 646 orthologous lncRNAs, provides information of the sequences, alignments, transposons, and species-specific insertions and deletions and allows database search on combinatorial conditions, graphic display and data download. As the first large-scale mammalian orthologous lncRNA database, LongMan has important values in future comparative and functional studies of lncRNAs.

相似文献/References:

[1]陈丽萍,黄载伟,肖冰.利用数据库分析胃食管反流病的发病因素与临床特点[J].南方医科大学学报,2016,(05):710.
[2]蒋洋洋,朱浩,张海.人类与小鼠同源lncRNA基因及其表观遗传调控靶基因分析[J].南方医科大学学报,2018,(06):731.
[3]戴余雷,颜禄斌,樊洁玲,等.尿液中的长链非编码RNA H19可协助诊断早期的急性肠坏死[J].南方医科大学学报,2018,(07):867.
[4]韩跃峰,陈德尚,李慧,等.长链非编码RNA MALAT-1基因的敲除抑制人喉鳞状细胞癌Hep-2细胞的增殖和迁移[J].南方医科大学学报,2018,(08):923.

更新日期/Last Update: 1900-01-01