TY - GEN
T1 - NCRNA homology search using Hamming distance seeds
AU - Aljawad, Osama
AU - Sun, Yanni
AU - Liu, Alex
AU - Lei, Jikai
N1 - Publication details (e.g. title, author(s), publication statuses and dates) are captured on an “AS IS” and “AS AVAILABLE” basis at the time of record harvesting from the data source. Suggestions for further amendments or supplementary information can be sent to [email protected].
PY - 2011
Y1 - 2011
N2 - 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. Copyright © 2011 ACM.
AB - 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. Copyright © 2011 ACM.
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U2 - 10.1145/2147805.2147828
DO - 10.1145/2147805.2147828
M3 - RGC 32 - Refereed conference paper (with host publication)
SN - 9781450307963
T3 - 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011
SP - 209
EP - 217
BT - 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011
T2 - 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011
Y2 - 1 August 2011 through 3 August 2011
ER -