TY - GEN
T1 - Constrained RNA structural alignment
T2 - 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
AU - Khaladkar, Mugdha
AU - Bellofatto, Vivian
AU - Wang, Jason
AU - Patel, Vandanaben
AU - Nakayama, Marvin
PY - 2007/12/1
Y1 - 2007/12/1
N2 - In this paper we propose a new method for aligning two RNA secondary structures by taking into account the presence of conserved RNA substructures, or constraints, in the alignment process. Our method allows the incorporation of specific knowledge about the RNA structures being analyzed while computing their alignment and thus is very useful for RNA motif detection. We develop statistical measures to assess the significance of alignment scores. Experimental results obtained by using the constrained alignment method to search for structural motifs in the untranslated regions of Trypanosoma brucei mRNAs demonstrate the good performance of the proposed method and its superiority over existing methods.
AB - In this paper we propose a new method for aligning two RNA secondary structures by taking into account the presence of conserved RNA substructures, or constraints, in the alignment process. Our method allows the incorporation of specific knowledge about the RNA structures being analyzed while computing their alignment and thus is very useful for RNA motif detection. We develop statistical measures to assess the significance of alignment scores. Experimental results obtained by using the constrained alignment method to search for structural motifs in the untranslated regions of Trypanosoma brucei mRNAs demonstrate the good performance of the proposed method and its superiority over existing methods.
UR - http://www.scopus.com/inward/record.url?scp=47649121789&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=47649121789&partnerID=8YFLogxK
U2 - 10.1109/BIBE.2007.4375585
DO - 10.1109/BIBE.2007.4375585
M3 - Conference contribution
AN - SCOPUS:47649121789
SN - 1424415098
SN - 9781424415090
T3 - Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
SP - 334
EP - 341
BT - Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
Y2 - 14 January 2007 through 17 January 2007
ER -