| Data name ⇅ | Database name ⇅ | DOI ⇅ | Description of data contents ⇅ | Data file ⇅ | Simple search URL ⇅ | Data acquisition method ⇅ | Data analysis method ⇅ | Number of data entries ⇅ | Data detail |
|---|---|---|---|---|---|---|---|---|---|
| The list of strains and growth conditions | The Rice Growth Monitoring for the Phenotypic Functional Analysis | 10.18908/lsdba.nbdc00945-001 |
The list of strains and growth conditions for respective samples. |
phenome_data.zip
(1KB) |
http://togodb.biosciencedbc.jp/togodb/view/agritogo_phenome_data_list#en | 7 entries |
Data detail
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| The rice growth image files | The Rice Growth Monitoring for the Phenotypic Functional Analysis | 10.18908/lsdba.nbdc00945-004 |
The rice growth image files categorized based on file size. |
image files (directory)
(233MB) |
- | 14 entries |
Data detail
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| Sequence Classification | TMBETA-GENOME | 10.18908/lsdba.nbdc00713-002 |
Results of predicting β-barrel membrane proteins or transmembrane helical proteins by applying statistical and machine learning methods to each amino acid sequence in the genomes. Statistical methods are based on amino acid composition, residue pair preference (dipeptide) and motifs (2 amino acid residues with an in-between residue gap). In machine learning methods, the combination of amino acid and dipeptide compositions has been used as main attributes. |
tmbeta_genome_sequence_classification.zip
(177 MB) |
http://togodb.biosciencedbc.jp/togodb/view/tmbeta_genome_sequence_classification#en |
Amino acid sequences were taken from the NCBI database. |
903,989 entries |
Data detail
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| Sequence Collection | TMBETA-GENOME | 10.18908/lsdba.nbdc00713-001 |
A collection of complete genomes annotated with β-barrel membrane protein predictions. For a genome that have multiple chromosomes, the entry set for each chormosome is given individually. |
tmbeta_genome_sequence_collection.zip
(8.8 KB) |
http://togodb.biosciencedbc.jp/togodb/view/tmbeta_genome_sequence_collection#en |
275 complete genomes, including 23 genomes from archaea, 237 from bacteria and 15 from eukaryote, were taken from the NCBI database. |
427 entries |
Data detail
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| TMFunction data | TMFunction | 10.18908/lsdba.nbdc00714-001 |
TMFunction is a database of functional residues in alpha-helical and beta-barrel membrane proteins. Each protein is identified with its name and source alongwith the UniProt code. The protein data bank (PDB) codes are also given for available proteins. Different methods and experimental parameters, for example, affinity, dissociation constant, IC50, activity etc. are given in the database. Further, we have provided the numerical experimental value for each residue (or mutant) in a protein. The experimental data are collected from the literature both by searching the journals as well as with the keyword search at PubMed. In addition, complete reference is given with journal citation and PMID number. |
tmfunction.zip
(48.5 KB) |
http://togodb.biosciencedbc.jp/togodb/view/tmfunction#en |
UniProt, PDB, PubMed |
2,907 entries |
Data detail
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| Data name | Database name | DOI | Description of data contents | Data file | Simple search URL | Data acquisition method | Data analysis method | Number of data entries | Data detail |
List of Data Metadata