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首页> 外文期刊>Journal of Molecular Biology >Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles
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Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles

机译：使用二级结构图谱直接从多个序列比对确定和鉴定RNA基序

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摘要

We present here a new approach to the problem of defining RNA signatures and finding their occurrences in sequence databases. TI-le proposed method is based on "secondary structure profiles". An RNA sequence alignment with secondary structure information is used as an input. Two types of weight matrices/profiles are constructed from this alignment: single strands are represented by a classical lod-scores profile while helical regions are represented by an extended "helical profile" comprising 16 lod-scores per position, one for each of the 16 possible base-pairs. Database searches are then conducted using a simultaneous search for helical profiles and dynamic programming alignment of single strand profiles. The algorithm has been implemented into a new software, ERPIN, that performs both profile construction and database search. Applications are presented for several RNA motifs. The automated use of sequence information in both single-stranded and helical regions yields better sensitivity/specificity ratios than descriptor-based programs. Furthermore, since the translation of alignments into profiles is straightforward with ERPIN, iterative searches can easily be conducted to enrich collections of homologous RNAs.
机译：我们在这里提出一种新方法来解决定义RNA签名并在序列数据库中发现它们的问题。 TI-le提出的方法基于“二级结构轮廓”。具有二级结构信息的RNA序列比对用作输入。从这种比对中可以构造出两种类型的权重矩阵/轮廓：单链由经典的lod-scores轮廓表示，而螺旋区域由扩展的“螺旋轮廓”表示，每个位置包括16个lod-score，每个16个lod-score可能的碱基对。然后使用同时搜索螺旋轮廓和单链轮廓的动态编程比对进行数据库搜索。该算法已被实施到新的软件ERPIN中，该软件可执行概要文件构建和数据库搜索。提出了几种RNA基序的应用。与基于描述符的程序相比，在单链和螺旋区域中序列信息的自动化使用都能产生更好的灵敏度/特异性比。此外，由于使用ERPIN可以将比对翻译成简档，因此可以轻松进行迭代搜索以丰富同源RNA的集合。

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