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| Content Provider | IEEE Xplore Digital Library |
|---|---|
| Author | Yogev, S. Milo, N. Ziv-Ukelson, M. |
| Copyright Year | 2013 |
| Description | Author affiliation: Dept. of Comput. Sci., Ben-Gurion Univ. of the Negev, Beer-Sheva, Israel (Yogev, S.; Milo, N.; Ziv-Ukelson, M.) |
| 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. |
| Sponsorship | IEEE Comput.Soc. |
| Starting Page | 145 |
| Ending Page | 152 |
| File Size | 450277 |
| Page Count | 8 |
| File Format | |
| ISBN | 9781479913091 |
| DOI | 10.1109/BIBM.2013.6732478 |
| Language | English |
| Publisher | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Publisher Date | 2013-12-18 |
| Publisher Place | China |
| Access Restriction | Subscribed |
| Rights Holder | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Subject Keyword | RNA Genomics Feature extraction Topology Bioinformatics Indexing |
| Content Type | Text |
| Resource Type | Article |
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