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SynBioLGDB: a resource for experimentally validated logic gates in synthetic biology.

Wang L, Qian K, Huang Y, Jin N, Lai H, Zhang T, Li C, Zhang C, Bi X, Wu D, Wang C, Wu H, Tan P, Lu J, Chen L, Li K, Li X, Wang D - Sci Rep (2015)

Bottom Line: Increasing evidence has also revealed that diverse genetic logic gates capable of generating a Boolean function play critically important roles in synthetic biology.Basic genetic logic gates have been designed to combine biological science with digital logic.SynBioLGDB will enable more comprehensive understanding of the connection of genetic logic gates to execute complex cellular functions in living cells.

View Article: PubMed Central - PubMed

Affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.

ABSTRACT
Synthetic biologists have developed DNA/molecular modules that perform genetic logic operations in living cells to track key moments in a cell's life or change the fate of a cell. Increasing evidence has also revealed that diverse genetic logic gates capable of generating a Boolean function play critically important roles in synthetic biology. Basic genetic logic gates have been designed to combine biological science with digital logic. SynBioLGDB (http://bioinformatics.ac.cn/synbiolgdb/) aims to provide the synthetic biology community with a useful resource for efficient browsing and visualization of genetic logic gates. The current version of SynBioLGDB documents more than 189 genetic logic gates with experimental evidence involving 80 AND gates and 16 NOR gates, etc. in three species (Human, Escherichia coli and Bacillus clausii). SynBioLGDB provides a user-friendly interface through which conveniently to query and browse detailed information about these genetic logic gates. SynBioLGDB will enable more comprehensive understanding of the connection of genetic logic gates to execute complex cellular functions in living cells.

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Related in: MedlinePlus

Flowchart for the Search page.(A) Screenshot of the three searching interfaces to retrieve SynBioLGDB; (B) Results of a representative entry.
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f3: Flowchart for the Search page.(A) Screenshot of the three searching interfaces to retrieve SynBioLGDB; (B) Results of a representative entry.

Mentions: SynBioLGDB provides a user-friendly interface for convenient data retrieval. Users can search each logic gate by three Paths (Figure 3): ‘By keyword' (search by any key information with support for fuzzy search); ‘By gene/protein/promoter' (select specific gene/protein/promoter symbols based on the input category with multiple selection supported); and ‘By gate category' (select the gate category of interest). Brief details of the search results are presented as a table in the ‘Result' page, while more detailed descriptions, such as the PMID and description of the reference, are displayed in the ‘Detail' page, reached by selecting ‘more'. When selecting the specific logic gate in the ‘Detail' page (Figure 4), the summary page presents more associated information about the logic gate, such as gate category, input categories, input gene/protein/promoter symbols, input gene/protein/promoter sequence, input promoter downstream gene symbol, input promoter downstream gene sequence, output category, species, validated method, PMID and detailed description.


SynBioLGDB: a resource for experimentally validated logic gates in synthetic biology.

Wang L, Qian K, Huang Y, Jin N, Lai H, Zhang T, Li C, Zhang C, Bi X, Wu D, Wang C, Wu H, Tan P, Lu J, Chen L, Li K, Li X, Wang D - Sci Rep (2015)

Flowchart for the Search page.(A) Screenshot of the three searching interfaces to retrieve SynBioLGDB; (B) Results of a representative entry.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4308699&req=5

f3: Flowchart for the Search page.(A) Screenshot of the three searching interfaces to retrieve SynBioLGDB; (B) Results of a representative entry.
Mentions: SynBioLGDB provides a user-friendly interface for convenient data retrieval. Users can search each logic gate by three Paths (Figure 3): ‘By keyword' (search by any key information with support for fuzzy search); ‘By gene/protein/promoter' (select specific gene/protein/promoter symbols based on the input category with multiple selection supported); and ‘By gate category' (select the gate category of interest). Brief details of the search results are presented as a table in the ‘Result' page, while more detailed descriptions, such as the PMID and description of the reference, are displayed in the ‘Detail' page, reached by selecting ‘more'. When selecting the specific logic gate in the ‘Detail' page (Figure 4), the summary page presents more associated information about the logic gate, such as gate category, input categories, input gene/protein/promoter symbols, input gene/protein/promoter sequence, input promoter downstream gene symbol, input promoter downstream gene sequence, output category, species, validated method, PMID and detailed description.

Bottom Line: Increasing evidence has also revealed that diverse genetic logic gates capable of generating a Boolean function play critically important roles in synthetic biology.Basic genetic logic gates have been designed to combine biological science with digital logic.SynBioLGDB will enable more comprehensive understanding of the connection of genetic logic gates to execute complex cellular functions in living cells.

View Article: PubMed Central - PubMed

Affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.

ABSTRACT
Synthetic biologists have developed DNA/molecular modules that perform genetic logic operations in living cells to track key moments in a cell's life or change the fate of a cell. Increasing evidence has also revealed that diverse genetic logic gates capable of generating a Boolean function play critically important roles in synthetic biology. Basic genetic logic gates have been designed to combine biological science with digital logic. SynBioLGDB (http://bioinformatics.ac.cn/synbiolgdb/) aims to provide the synthetic biology community with a useful resource for efficient browsing and visualization of genetic logic gates. The current version of SynBioLGDB documents more than 189 genetic logic gates with experimental evidence involving 80 AND gates and 16 NOR gates, etc. in three species (Human, Escherichia coli and Bacillus clausii). SynBioLGDB provides a user-friendly interface through which conveniently to query and browse detailed information about these genetic logic gates. SynBioLGDB will enable more comprehensive understanding of the connection of genetic logic gates to execute complex cellular functions in living cells.

Show MeSH
Related in: MedlinePlus