We present a novel dynamic programming framework that allows one to compute tight upper bounds for the p-values of gapped local alignments in pseudo–polynomial time. Our algorith...
Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers succes...
Knowledge of energy barriers between pairs of secondary structures for a given DNA or RNA molecule is useful, both in understanding RNA function in biological settings and in desig...
— This paper presents an approach to the multiple sequence alignment (MSA) problem by applying genetic algorithms with a reserve selection mechanism. MSA is one of the most funda...
Yang Chen, Jinglu Hu, Kotaro Hirasawa, Songnian Yu
1 Profile Hidden Markov Models (profile HMMs) are used as a popular bioinformatics tool for sensitive database searching, e.g. a set of not annotated protein sequences is compared...