We propose an iterative probabilistic algorithm for estimation of RNA secondary structure using sequence data from two homologous sequences. The method is intended to exploit inte...
Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathe...
Abstract. Local similarity is an important tool in comparative analysis of biological sequences, and is therefore well studied. In particular, the Smith-Waterman technique and its ...
Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren...
Background: Joint alignment and secondary structure prediction of two RNA sequences can significantly improve the accuracy of the structural predictions. Methods addressing this p...
Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathe...
Background: Non-coding RNAs (ncRNAs) have a multitude of roles in the cell, many of which remain to be discovered. However, it is difficult to detect novel ncRNAs in biochemical s...
Andrew V. Uzilov, Joshua M. Keegan, David H. Mathe...
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A, C, G, U}. The higher structure i...