FastR: fast database search tool for non-coding RNA.

Proceedings. IEEE Computational Systems Bioinformatics Conference Pub Date : 2004-01-01 DOI:10.1109/csb.2004.1332417

Vineet Bafna, Shaojie Zhang

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Abstract

The discovery of novel non-coding RNAs has been among the most exciting recent developments in Biology. Yet, many more remain undiscovered. It has been hypothesized that there is in fact an abundance of functional non-coding RNA (ncRNA) with various catalytic and regulatory functions. Computational methods tailored specifically for ncRNA are being actively developed. As the inherent signal for ncRNA is weaker than that for protein coding genes, comparative methods offer the most promising approach, and are the subject of our research. We consider the following problem: Given an RNA sequence with a known secondary structure, efficiently compute all structural homologs (computed as a function of sequence and structural similarity) in a genomic database. Our approach, based on structural filters that eliminate a large portion of the database, while retaining the true homologs allows us to search a typical bacterial database in minutes on a standard PC, with high sensitivity and specificity. This is two orders of magnitude better than current available software for the problem.

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FastR:非编码RNA的快速数据库搜索工具。

新的非编码rna的发现是生物学最近最令人兴奋的发展之一。然而，还有更多尚未被发现。据推测，实际上存在大量具有各种催化和调节功能的功能性非编码RNA (ncRNA)。目前正在积极开发专门针对ncRNA的计算方法。由于ncRNA的固有信号弱于蛋白质编码基因，比较方法是最有希望的方法，也是我们研究的主题。我们考虑以下问题:给定具有已知二级结构的RNA序列，有效地计算基因组数据库中所有结构同源性(作为序列和结构相似性的函数计算)。我们的方法，基于结构过滤器，消除了数据库的很大一部分，同时保留了真正的同源物，使我们能够在几分钟内在标准PC上搜索一个典型的细菌数据库，具有高灵敏度和特异性。这比目前可用的解决该问题的软件好两个数量级。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Proceedings. IEEE Computational Systems Bioinformatics Conference

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