title: dbCRY: a Web-based comparative and evolutionary genomics platform for blue-light receptors.
abstract: Cryptochromes are flavoproteins that play a central role in the circadian oscillations of all living organisms except archaea. Cryptochromes are clustered into three subfamilies: plant-type cryptochromes, animal-type cryptochromes and cryptochrome-DASH proteins. These subfamilies are composed of photolyase/cryptochrome superfamily with 6-4 photolyase and cyclobutane pyrimidine dimer photolyase. Cryptochromes have conserved domain architectures with two distinct domains, an N-terminal photolyase-related domain and a C-terminal domain. Although the molecular function and domain architecture of cryptochromes are conserved, their molecular mechanisms differ between plants and animals. Thus, cryptochromes are one of the best candidates for comparative and evolutionary studies. Here, we have developed a Web-based platform for comparative and evolutionary studies of cryptochromes, dbCRY (http://www.dbcryptochrome.org/). A pipeline built upon the consensus domain profile was applied to 1438 genomes and identified 1309 genes. To support comparative and evolutionary genomics studies, the Web interface provides diverse functions such as (i) browsing by species, (ii) protein domain analysis, (iii) multiple sequence alignment, (iv) homology search and (v) extended analysis opportunities through the implementation of 'Favorite Browser' powered by the Comparative Fungal Genomics Platform 2.0 (CFGP 2.0; http://cfgp.snu.ac.kr/). dbCRY would serve as a standardized and systematic solution for cryptochrome genomics studies. Database URL: http://www.dbcryptochrome.org/
authors.affiliation: Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Bioinformatics and Life Science, Soongsil University, Seoul 156-743, Korea and Center for Fungal Genetic Resources and Center for Fungal Pathogenesis, Seoul National University, Seoul 151-742, Korea.
authors.forename: Yong-Min
authors.initials: YM
authors.lastname: Kim
authors.forename: Jaeyoung
authors.initials: J
authors.lastname: Choi
authors.forename: Hye-Young
authors.initials: HY
authors.lastname: Lee
authors.forename: Gir-Won
authors.initials: GW
authors.lastname: Lee
authors.forename: Yong-Hwan
authors.initials: YH
authors.lastname: Lee
authors.forename: Doil
authors.initials: D
authors.lastname: Choi
mesh_terms: D019295:Computational Biology / Q000379:methods*; D056931:Cryptochromes / Q000737:chemistry / Q000145:classification / Q000235:genetics; D030541:Databases, Genetic; D019143:Evolution, Molecular; D020407:Internet; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein
chemical_list: D056931:Cryptochromes