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dbCRY: a Web-based comparative and evolutionary genomics platform for blue-light receptors.

Kim YM, Choi J, Lee HY, Lee GW, Lee YH, Choi D - Database (Oxford) (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

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.

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/

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A screenshot of the Favorite Browser in dbCRY. Users are able to collect genes and investigate their domain architectures (red box) or composition of the genes of interest (blue box). The sequences can be downloaded with options of a full-length or a specific domain based on InterPro accessions (orange box). Users can also conduct DNA/protein alignments or phylogenetic analyses, and these results can also be downloaded.
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bau037-F3: A screenshot of the Favorite Browser in dbCRY. Users are able to collect genes and investigate their domain architectures (red box) or composition of the genes of interest (blue box). The sequences can be downloaded with options of a full-length or a specific domain based on InterPro accessions (orange box). Users can also conduct DNA/protein alignments or phylogenetic analyses, and these results can also be downloaded.

Mentions: dbCRY provides various functions via Favorite, a personalized data repository and analysis hub featured by the Comparative Fungal Genomics Platform (CFGP 2.0, http://cfgp.snu.ac.kr/) (22). dbCRY provides (i) class distribution, (ii) protein domain browser, (iii) domain sequence retrieval, (iv) homology search tools (BLAST and BLASTMatrix) and (v) a multiple sequence alignment tool (ClustalW; Figure 3). In particular, the domain sequence retrieval and multiple sequence alignment tools facilitate the search for conserved residues in the specific domains of selected cryptochromes. The Favorites created in dbCRY can be used in CFGP 2.0, which offers flexible and extended analysis options for further analysis. In addition, the Favorites are also interconnected with a number of gene family databases to offer multigene family analysis opportunities.Figure 3.


dbCRY: a Web-based comparative and evolutionary genomics platform for blue-light receptors.

Kim YM, Choi J, Lee HY, Lee GW, Lee YH, Choi D - Database (Oxford) (2014)

A screenshot of the Favorite Browser in dbCRY. Users are able to collect genes and investigate their domain architectures (red box) or composition of the genes of interest (blue box). The sequences can be downloaded with options of a full-length or a specific domain based on InterPro accessions (orange box). Users can also conduct DNA/protein alignments or phylogenetic analyses, and these results can also be downloaded.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4016680&req=5

bau037-F3: A screenshot of the Favorite Browser in dbCRY. Users are able to collect genes and investigate their domain architectures (red box) or composition of the genes of interest (blue box). The sequences can be downloaded with options of a full-length or a specific domain based on InterPro accessions (orange box). Users can also conduct DNA/protein alignments or phylogenetic analyses, and these results can also be downloaded.
Mentions: dbCRY provides various functions via Favorite, a personalized data repository and analysis hub featured by the Comparative Fungal Genomics Platform (CFGP 2.0, http://cfgp.snu.ac.kr/) (22). dbCRY provides (i) class distribution, (ii) protein domain browser, (iii) domain sequence retrieval, (iv) homology search tools (BLAST and BLASTMatrix) and (v) a multiple sequence alignment tool (ClustalW; Figure 3). In particular, the domain sequence retrieval and multiple sequence alignment tools facilitate the search for conserved residues in the specific domains of selected cryptochromes. The Favorites created in dbCRY can be used in CFGP 2.0, which offers flexible and extended analysis options for further analysis. In addition, the Favorites are also interconnected with a number of gene family databases to offer multigene family analysis opportunities.Figure 3.

Bottom Line: 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.

View Article: PubMed Central - PubMed

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.

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/

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