General information of database
Laboratory of Plant Functional Genomics, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo
|Protein sequence databases|
Taxonomy Name:11 plants, 9 Other bikonts, 25 cyanobacteria, 15 photosynthetic bacteria, 31 non-photosynthetic bacteria, 8 Opistokonts (animals and fungi), total 95 species
Database of sequence clusters obtained as a result of all-against-all BLAST search of proteins in 95 organism species.
Gclust is characterized by the capacity to perform classification of homologous proteins with automatically setting the threshold of similarity based on the results of the BLAST search of all proteins of all organism species to be compared. Because a homologous culster can be generated even for proteins with unknown function, Gclust may also be useful to find proteins which play important roles for a particular organisms or taxa of interest through such a generated homologous cluster specific to the organisms or taxa. (phylogenetic profiling).
Sequence comparison of homologous proteins across many organisms is the very basic of comparative genomics, but pairwise intergenomic comparison has been conventional. Degrees of sequence conservation depend on protein groups;some protein groups are highly conserved, but some orthologs are poorly conserved. Considering these points, we developed a technique which automatically generates ortholog clusters, and applied the technique to functional analysis of protein groups specific to photosynthetic organisms.
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