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dbCRY: a Web-based comparative and evolutionary genomics platform for blue-light receptors
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 Authours
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Yong-Min Kim, Jaeyoung Choi, Hye-Young Lee, Gir-Won Lee, Yong-Hwan Lee and Doil Choi |
| Title |
dbCRY: a Web-based comparative and evolutionary genomics platform for blue-light receptors |
| Journal |
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2014 (2014) ~ |
Abstract
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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. |
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