MapMi: automated mapping of microRNA loci.
MapMi: automated mapping of microRNA loci.
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DOI：
10.1186/1471-2105-11-133
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发表时间：
2010-03-16
影响因子：
3
通讯作者：
Enright AJ
中科院分区：
文献类型：
--
作者：
Guerra-Assunção JA;Enright AJ
发现microRNAs（miRNAs）的巨大努力已经展开。目前，miRBase是他们的主要知识库，提供一级序列，前体和可能的基因组位点的注释。在许多情况下，miRNA在相关（或在某些情况下更远）物种之间是相同或非常相似的。然而，miRBase专注于那些已经直接证实了miRNAs的物种。其次，即使在覆盖良好的物种中，特定的miRNA或其位点有时也没有注释。我们试图解决这个问题，通过开发一个计算系统，自动映射的miRNAs内和跨物种。给定一个物种中已知的miRNA的序列，确定该miRNA在其他物种中的可能位点是相对简单的。我们的主要目标不是发现新的miRNAs，而是将一个物种中经过验证的miRNAs映射到其他物种中最可能的直系同源物。我们提出了MapMi，一个跨物种和物种内的自动化miRNA映射的计算系统。该方法的敏感性为92.20%，特异性为97.73%。使用miRBase的最新版本（v14），当MapMi应用于Ensembl Metazoa版本2中的所有21个物种和Ensembl版本55中的46个物种时，我们获得了10，944个未注释的潜在miRNA。用于绘制miRNA的管道和相关网络服务器可在http://www.ebi.ac.uk/enright-srv/MapMi/上免费获得。此外，提供了跨大量物种的miRBase miRNA的预先计算的miRNA映射。
A large effort to discover microRNAs (miRNAs) has been under way. Currently miRBase is their primary repository, providing annotations of primary sequences, precursors and probable genomic loci. In many cases miRNAs are identical or very similar between related (or in some cases more distant) species. However, miRBase focuses on those species for which miRNAs have been directly confirmed. Secondly, specific miRNAs or their loci are sometimes not annotated even in well-covered species. We sought to address this problem by developing a computational system for automated mapping of miRNAs within and across species. Given the sequence of a known miRNA in one species it is relatively straightforward to determine likely loci of that miRNA in other species. Our primary goal is not the discovery of novel miRNAs but the mapping of validated miRNAs in one species to their most likely orthologues in other species. We present MapMi, a computational system for automated miRNA mapping across and within species. This method has a sensitivity of 92.20% and a specificity of 97.73%. Using the latest release (v14) of miRBase, we obtained 10,944 unannotated potential miRNAs when MapMi was applied to all 21 species in Ensembl Metazoa release 2 and 46 species from Ensembl release 55. The pipeline and an associated web-server for mapping miRNAs are freely available on http://www.ebi.ac.uk/enright-srv/MapMi/. In addition precomputed miRNA mappings of miRBase miRNAs across a large number of species are provided.
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影响因子：
5.8
作者：
Waterhouse, Andrew M.;Procter, James B.;Barton, Geoffrey J.
通讯作者：
Barton, Geoffrey J.
影响因子：
56.9
作者：
Giraldez, AJ;Mishima, Y;Schier, AF
通讯作者：
Schier, AF
Mirbase：MicroRNA基因组学的工具。
影响因子：
14.9
作者：
Griffiths-Jones, Sam;Saini, Harpreet Kaur;van Dongen, Stijn;Enright, Anton J.
通讯作者：
Enright, Anton J.
影响因子：
14.9
作者：
Gerlach D;Kriventseva EV;Rahman N;Vejnar CE;Zdobnov EM
通讯作者：
Zdobnov EM
影响因子：
14.9
作者：
Chang, Tzu-Hao;Horng, Jorng-Tzong;Huang, Hsien-Da
通讯作者：
Huang, Hsien-Da