Nucleic Acids Research Advance Access originally published online on January 7, 2009
Nucleic Acids Research 2009 37(3):999-1009; doi:10.1093/nar/gkn1054
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2009, Vol. 37, No. 3 999-1009
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Computational Biology |
Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans
1Department of Biosciences and Informatics, Keio University, 3–14–1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223–8522, 2Japan Biological Informatics Consortium (JBIC), 2–45 Aomi, Koto-ku, Tokyo 135–8073 and 3Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2–42 Aomi, Koto-ku, Tokyo 135–0064, Japan
*To whom correspondence should be addressed. Tel: +81 45 566 1791; Fax: +81 45 566 1791; Email: yasu{at}bio.keio.ac.jp
Received July 3, 2008. Revised November 25, 2008. Accepted December 17, 2008.
Despite the accumulating research on noncoding RNAs (ncRNAs), it is likely that we are seeing only the tip of the iceberg regarding our understanding of the functions and the regulatory roles served by ncRNAs in cellular metabolism, pathogenesis and host-pathogen interactions. Therefore, more powerful computational and experimental tools for analyzing ncRNAs need to be developed. To this end, we propose novel kernel functions, called base-pairing profile local alignment (BPLA) kernels, for analyzing functional ncRNA sequences using support vector machines (SVMs). We extend the local alignment kernels for amino acid sequences in order to handle RNA sequences by using STRAL's; scoring function, which takes into account sequence similarities as well as upstream and downstream base-pairing probabilities, thus enabling us to model secondary structures of RNA sequences. As a test of the performance of BPLA kernels, we applied our kernels to the problem of discriminating members of an RNA family from nonmembers using SVMs. The results indicated that the discrimination ability of our kernels is stronger than that of other existing methods. Furthermore, we demonstrated the applicability of our kernels to the problem of genome-wide search of snoRNA families in the Caenorhabditis elegans genome, and confirmed that the expression is valid in 14 out of 48 of our predicted candidates by using qRT-PCR. Finally, highly expressed six candidates were identified as the original target regions by DNA sequencing.
Present address: Kensuke Morita, IBM Japan, Ltd. 19–21 Nihonbashi Hakozaki-cho, Chuo-ku, Tokyo 103–8510, Japan
The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors.