RNATOPS-W: a web server for RNA structure searches of genomes.
RNATOPS-W: a web server for RNA structure searches of genomes.
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RNATOPS-W：用于基因组 RNA 结构搜索的网络服务器。
DOI：
10.1093/bioinformatics/btp095
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发表时间：
2009
期刊：
影响因子：
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通讯作者：
Cai,Liming
中科院分区：
文献类型：
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作者：
Wang,Yingfeng;Huang,Zhibin;Wu,Yong;Malmberg,RussellL;Cai,Liming
摘要：RNATOPS-W是一个网络服务器，用于搜索RNA二级结构序列，包括假结。服务器接受注释的RNA多重结构比对作为结构概况和基因组或其他序列进行搜索。它是建立在RNATOPS之上的，RNATOPS是一个用于相同目的的命令行C++软件包，其中可以手动选择加速搜索的过滤器。RNATOPS-W通过添加隐马尔可夫模型（HMM）滤波器的自动选择功能以及用户选择子结构滤波器的友好用户界面来改进RNATOPS。此外，RNATOPS-W补充了现有的RNA二级结构搜索网络服务器，这些服务器要么使用内置的结构配置文件，要么无法检测伪结。RNATOPS-W继承了RNATOPS在检测大型复杂RNA结构方面的效率。可用性：网络服务器RNATOPS-W可在网站www.uga.edu/RNA-Informatics/?上获得f=软件&p=RNATOPS-w。基础搜索程序RNATOPS可从www.uga.edu/RNA-Informatics/?下载f=software&p=RNATOPS。联系方式：cai@cs.uga. edu补充信息：补充数据可在Bioinformatics online获取。
Summary:RNATOPS-W is a web server to search sequences for RNA secondary structures including pseudoknots. The server accepts an annotated RNA multiple structural alignment as a structural profile and genomic or other sequences to search. It is built upon RNATOPS, a command line C++software package for the same purpose, in which filters to speed up search are manually selected. RNATOPS-W improves upon RNATOPS by adding the function of automatic selection of a hidden Markov model (HMM) filter and also a friendly user interface for selection of a substructure filter by the user. In addition, RNATOPS-W complements existing RNA secondary structure search web servers that either use built-in structure profiles or are not able to detect pseudoknots. RNATOPS-W inherits the efficiency of RNATOPS in detecting large, complex RNA structures.Availability:The web server RNATOPS-W is available at the web site www.uga.edu/RNA-Informatics/?f=software&p=RNATOPS-w. The underlying search program RNATOPS can be downloaded at www.uga.edu/RNA-Informatics/?f=software&p=RNATOPS.Contact:cai@cs.uga.eduSupplementary information:Supplementary data are available atBioinformaticsonline.