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...
Motivation: Non-coding RNAs (ncRNAs)--functional RNA molecules not coding for proteins--are grouped into hundreds of families of homologs. To find new members of an ncRNA gene fam...
We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent wi...
The discovery of novel non-coding RNAs has been among the most exciting recent developments in Biology. Yet, many more remain undiscovered. It has been hypothesized that there is ...
Background: The general problem of RNA secondary structure prediction under the widely used thermodynamic model is known to be NP-complete when the structures considered include a...