StemSearch: RNA Search Tool Based on Stem Identification and Indexing

Sivan Yogev, Nimrod Milo, Michal Ziv-Ukelson

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

The discovery and functional analysis of noncoding RNA (ncRNA) systems in different organisms motivates the development of tools for aiding ncRNA research. Several tools exist that search for occurrences of a given RNA structural profile in genomic sequences. Yet, there is a need for an 'RNA BLAST' tool, i.e. a tool that takes a putative functional RNA sequence as input, and efficiently searches for similar sequences in genomic databases, taking into consideration potential secondary structure features of the input query sequence. This work aims at providing such a tool. Our tool, denoted StemSearch, is based on a structural representation of an RNA sequence by its potential stems. Potential stems in genomic sequences are identified in a preprocessing stage, and indexed. A user provided query sequence is likewise processed, and stems from the target genomes which are similar to the query stems are retrieved from the index. Then, relevant genomic regions are identified and ranked according to their similarity to the query stem-set while enforcing conservation of cross-stem topology. Experiments using RFAM families show significantly improved recall for StemSearch over BLAST, with small loss of precision. We further demonstrate our system's capability to handle eukaryotic genomes by successfully searching for members of the 7SK family in chromosome 2 of the human genome. StemSearch is freely available on the web at: http://www.cs.bgu. ac.il/~negevcb/StemSearch

Original languageEnglish
Title of host publicationProceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013
Pages145-152
Number of pages8
DOIs
StatePublished - 1 Dec 2013
Event2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013 - Shanghai, China
Duration: 18 Dec 201321 Dec 2013

Conference

Conference2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013
Country/TerritoryChina
CityShanghai
Period18/12/1321/12/13

ASJC Scopus subject areas

  • Biomedical Engineering

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