We study the problem of similarity detection by sequence alignment with gaps, using a recently established theoretical framework based on the morphology of alignment paths. Alignm...
Background: The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for ...
Rodrigo Gouveia-Oliveira, Peter Wad Sackett, Ander...
Background: While multiple alignment is the first step of usual classification schemes for biological sequences, alignment-free methods are being increasingly used as alternatives...
Eduardo Corel, Florian Pitschi, Ivan Laprevotte, G...
Background: Detection of common evolutionary origin (homology) is a primary means of inferring protein structure and function. At present, comparison of protein families represent...
We propose a method for finding seeds for the local alignment of two nucleotide sequences. Our method uses randomized algorithms to find approximate seeds. We present a dynamic ...