Designing seeds for similarity search in genomic DNA
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Designing multiple simultaneous seeds for DNA similarity search
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Bioinformatics
Chain-RNA: A Comparative ncRNA Search Tool Based on the Two-Dimensional Chain Algorithm
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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NcRNAs play important roles in many biological processes. Existing genome-scale ncRNA homology search tools identify ncRNAs in local sequence alignments generated by conventional sequence comparison methods. However, some types of ncRNA lack strong sequence conservation and tend to be missed by conventional sequence comparison methods. In this paper, we propose an ncRNA identification framework that is complementary to existing sequence comparison tools. By integrating a filtration step based on Hamming distance and a local structural alignment program such as FOLDALIGN, we can identify ncRNAs that lack strong sequence conservation. We introduce a coding method by which the Hamming-distance based filtration can easily distinguish transition from transversion, which show different frequency in functional ncRNAs. Our experiments demonstrate that the carefully designed Hamming distance seed can achieve better sensitivity in searching for poorly conserved ncRNAs than conventional sequence comparison tools.