Biological network alignment aims to find regions of topological and functional (dis)similarities between molecular networks of different species. Then, network alignment can guide the transfer of biological knowledge from well-studied model species to less well-studied species between conserved (aligned) network regions, thus complementing valuable insights that have already been provided by g...

With the rapid development of DNA sequencer, the rate of data generation is rapidly outpacing the rate at which it can be computationally processed. Traditional sequence alignment based on PC cannot fulfill the increasing demand. Accelerating the algorithm using FPGA provides the better performance compared to the other platforms. This paper will explain and classify the current sequence alignm...

In this paper we present a new method for aligning large sets of biological sequences. The method performs a sequence alignment in parallel and uses a decentralized cache to store intermediate results. The method allows alignments to be recomputed efficiently when new sequences are added or when alignments of different precisions are requested. Our method can be used to solve important biologic...

In this paper we present a procedure to refine the recognition dictionary based on a composite approach to prune the unneeded pronunciations. First, pruning is applied in a non-uniform manner according to the characteristics of each word. Even though this straightforward operation may produce high-quality dictionaries, it makes the refined dictionary heavily dependent on the data used in this p...

Multiple sequence alignment is a key process in today’s biology, and finding a relevant alignment of several sequences is much more challenging than just optimizing some improbable evaluation functions. Our approach for addressing multiple sequence alignment focuses on the building of structures in a new graph model: the factor graph model. This model relies on block-based formulation of the or...

MOTIVATION We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a structure superposition. APDB is designed to efficiently and objectively benchmark multiple sequence alignment methods. RESULTS Using existing collections of reference multiple sequence alignments...

conclusions the b3, b5, b7, b8 and b9 subgenotypes can be clustered into quasi-sub-genotype b3 and the open reading frame of hbv has a start codon preference; however, whether a mutation in the start codon in the pre-s2 region has an impact on survival and replication of hbv remains to be determined. background the number of cases of hbv infection reported by the who for each district and count...

To date, few attempts have been made to benchmark the alignment algorithms upon nucleic acid sequences. Frequently, sophisticated PAM or BLOSUM like models are used to align proteins, yet equivalents are not considered for nucleic acids; instead, rather ad hoc models are generally favoured. Here, we systematically test the performance of existing alignment algorithms on structural RNAs. This wo...