Multiple sequence alignment is the most fundamental task in bioinformatics and computational biology. In this paper, we present a new algorithm to conduct multiple sequences align...
We have recently demonstrated (La et al, Proteins, 58:2005) that sequence fragments approximating the overall familial phylogeny, called phylogenetic motifs (PMs), represent a pro...
Background: The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence ...
Background: When analyzing protein sequences using sequence similarity searches, orthologous sequences (that diverged by speciation) are more reliable predictors of a new protein&...
Peptide compositions constructed out of whole sets of protein sequences can be used as species signatures for phylogenetic analysis. To account for point mutations, an amino acid ...