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The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The database is unique in two respects: first, because of its phylogenetic position, Ciona is suitable model for understanding vertebrate evolution; and second, the database includes original large-scale transcriptomic and proteomic(More)
A trim distance is a measure for comparing positions in nucleotide sequences based on phylogenetic trees. In this paper, first we formulate another trim distance based on the MAST distance, in contrast to the previous trim distance based on the LCA-preserving distance. Next, we apply a group average method in agglomerative hierarchical clustering to the(More)
A large number of nucleotide sequences of various pathogens are available in public databases. The growth of the datasets has resulted in an enormous increase in computational costs. Moreover, due to differences in surveillance activities, the number of sequences found in databases varies from one country to another and from year to year. Therefore, it is(More)
A trim distance as a phylogeny-based distance between two positions in nucleotide sequences is formulated as an LCA-preserving distance between the trimmed phylogenetic trees by the positions. In this paper, in order to investigate the positions as packaging signals of nucleotide sequences in influenza A (H3N2) viruses, we compute and compare the trim(More)
CIPRO database (http://cipro.ibio.jp/2.5) is an integrated protein database for a tunicate species Ciona intestinalis that is part of the Urochordata. Although CIPRO provides proteomic and transcriptomic data on a single species , the animal is considered unique in the evolutionary tree, representing a possible origin of the vertebrates and is a good model(More)