NucBase, an easy to use read mapper for small RNAs.
NucBase, an easy to use read mapper for small RNAs.
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DOI：
10.1186/1759-8753-4-1
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发表时间：
2013-01-01
期刊：
影响因子：
4.9
通讯作者：
Vaury C
中科院分区：
文献类型：
--
作者：
Dufourt J;Pouchin P;Peyret P;Brasset E;Vaury C
高通量深度测序技术产生了前所未有的表达序列读数，为深入了解生物系统提供了机会。几个数据库报道了在转座因子（TE）的控制中起重要作用的小调控RNA的序列。然而，这些数据库中报告的大量数据大多未被探索，因为生物学家很难使用可用的工具。在这里，我们报告NucBase，一个新的程序，旨在进行详尽的搜索序列匹配，并从大型核酸数据库的基因组或输入序列比对短序列读取。NucBase包括一个图形界面，使生物学家能够轻松地比对序列，并立即可视化匹配的序列，它们的数量和基因组位置。NucBase识别与输入序列具有严格同一性的核酸基序，并且它能够找到具有一个或多个错配的候选物。它提供了鉴定由选定数量的连续匹配核苷酸组成的“核心序列”的机会。该软件可以在任何Windows、Linux或Mac OS计算机上本地运行，具有32位架构兼容性。由于该软件易于使用，并且可以检测其他软件未检测到的读数，我们相信它将对参与小型非编码RNA TE沉默领域的生物学家有用。我们希望NucBase将对更大的研究人员社区有用，因为它使探索任何生物体中的小核酸序列变得更加容易。
High-throughput deep-sequencing technology has generated an unprecedented number of expressed sequence reads that offer the opportunity to get insight into biological systems. Several databases report the sequence of small regulatory RNAs which play a prominent role in the control of transposable elements (TE). However, the huge amount of data reported in these databases remains mostly unexplored because the available tools are hard for biologists to use. Here we report NucBase, a new program designed to make an exhaustive search for sequence matches and to align short sequence reads from large nucleic acid databases to genomes or input sequences. NucBase includes a graphical interface which allows biologists to align sequences with ease and immediately visualize matched sequences, their number and their genomic position. NucBase identifies nucleic motives with strict identity to input sequences, and it capably finds candidates with one or several mismatches. It offers the opportunity to identify “core sequences” comprised of a chosen number of consecutive matching nucleotides. This software can be run locally on any Windows, Linux or Mac OS computer with 32-bit architecture compatibility. Since this software is easy to use and can detect reads that were undetected by other software, we believe that it will be useful for biologists involved in the field of TE silencing by small non-coding RNAs. We hope NucBase will be useful for a larger community of researchers, since it makes exploration of small nucleic sequences in any organism much easier.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
3
作者：
Ferragina P;Giancarlo R;Greco V;Manzini G;Valiente G
通讯作者：
Valiente G
DOI：
10.1093/bioinformatics/btp698
发表时间：
2010-03-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Li H;Durbin R
通讯作者：
Durbin R
影响因子：
64.5
作者：
Brennecke, Julius;Aravin, Alexei A.;Hannon, Gregory J.
通讯作者：
Hannon, Gregory J.
影响因子：
11.8
作者：
Carmell, Michelle A.;Girard, Angelique;Hannon, Gregory J.
通讯作者：
Hannon, Gregory J.