Muller Sébastien, Charpentier Bruno, Branlant Christiane, Leclerc Fabrice
Laboratoire de Maturation des ARN et Enzymologie Moléculaire, Nancy Université, Faculté des Sciences et Techniques, Vandoeuvre-les-Nancy, France.
Methods Enzymol. 2007;425:355-87. doi: 10.1016/S0076-6879(07)25015-3.
Whereas dedicated computational approaches have been developed for the search of C/D sRNAs and snoRNAs, as yet no dedicated computational approach has been developed for the search of archaeal H/ACA sRNAs. Here we describe a computational approach allowing a fast and selective identification of H/ACA sRNAs in archaeal genomes. It is easy to use, even for biologists having no special expertise in computational biology. This approach is a stepwise knowledge-based approach, combining the search for common structural features of H/ACA motifs and the search for their putative target sequences. The first step is based on the ERPIN software. It depends on the establishment of a secondary structure-based "profile." We explain how this profile is built and how to use ERPIN to optimize the search for H/ACA motifs. Several examples of applications are given to illustrate how powerful the method is, its limits, and how the results can be evaluated. Then, the possible target rRNA sequences corresponding to the identified H/ACA motifs are searched by use of a descriptor-based method (RNAMOT). The principles and the practical aspects of this method are also explained, and several examples are given here as well to help users in the interpretation of the results.
尽管已经开发出专门的计算方法用于搜索C/D型小RNA和核仁小RNA，但尚未开发出专门用于搜索古菌H/ACA小RNA的计算方法。在此，我们描述了一种计算方法，可快速、选择性地鉴定古菌基因组中的H/ACA小RNA。该方法易于使用，即使对于在计算生物学方面没有专业知识的生物学家也是如此。此方法是一种基于知识的逐步方法，结合了对H/ACA基序共同结构特征的搜索及其推定靶序列的搜索。第一步基于ERPIN软件。它依赖于基于二级结构的“图谱”的建立。我们解释了该图谱是如何构建的，以及如何使用ERPIN来优化对H/ACA基序的搜索。给出了几个应用示例，以说明该方法的强大之处、其局限性以及如何评估结果。然后，通过使用基于描述符的方法（RNAMOT）搜索与已鉴定的H/ACA基序相对应的可能靶rRNA序列。还解释了该方法的原理和实际应用方面，并在此给出了几个示例以帮助用户解释结果。
