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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
Table of Cluster and Organism Species Number Gclust Server 10.18908/lsdba.nbdc00464-010

Cluster, representative sequence ID of cluster, its length, the number of sequences contained in the cluster, organism species, the number of sequences belonging to the cluster for each of 95 organism species, compiled into a tab-delimited text file format table.

 all95.tbl.zip
(4.53MB) 		-

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Data detail open_in_full
Gene Name Thesaurus Gene Name Thesaurus 10.18908/lsdba.nbdc00966-001

Curators who have expertize in biological research edit gene names found in various databases and articles to show associations between them.

 dictionary.zip
(4.6MB) 		http://togodb.biosciencedbc.jp/togodb/view/lsdb_gene_thesaurus#en

We extracted synonyms described in databases such as Entrez Gene, Swiss-Prot and HGNC.

1. Collect gene names automatically from synonym information fields in various gene/genome databases.
2. The curators who have expertise in biological research confirm the name variation for genes and associate them. They also delete names which are confusing to associate (polysemy, acronyms for different genes etc.).
3. Extract words describe gene names from MEDLINE abstracts and collect unregistered names.
4. Evaluate detection performance of gene names in the dictionary.
5. Add non-detected words to the dictionary and repeat 4-5 using other literature set.

 Gene family Number of genes: 12,110 Number of names: 27,923 Human Number of genes: 27,959 Number of names: 145,623 Mouse Number of genes: 48,545 Number of names: 173,375 Rat Number of genes: 17,319 Number of names: 61,801 Zebrafish Number of genes: 24,230 Number of names: 60,270 Fruit fly Number of genes: 30,708 Number of names: 96,934 Nematode Number of genes: 25,304 Number of names: 96,220 Budding yeast Number of genes: 7,359 Number of names: 29,533 Fission yeast Number of genes: 7,943 Number of names: 15,431 Bacillus subtilis Number of genes: 4,206 Number of names: 14,816
Data detail open_in_full
HTML Source GENIUS II 10.18908/lsdba.nbdc00471-001

HTML Source of the original site (terminated). Note that links to CGI don't work.

 HTML_Source.tar.gz
(41MB) 		-

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Data detail open_in_full
ORF Alignment GENIUS II 10.18908/lsdba.nbdc00471-005

It links to the alingment information between ORF and intermediate sequences

 genius_orf_alignment.zip
(170 MB) 		https://togodb.biosciencedbc.jp/togodb/view/genius_orf_alignment#en

RefSeq, nr-aa

We conducted BLAST search between ORF and intermediate sequences (nr-aa).

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Data detail open_in_full
ORF List GENIUS II 10.18908/lsdba.nbdc00471-002

This is the ORF list of 234 genomes. You can access to ORF sequences and these alignments information.

 genius_orf_list.zip
(15 MB) 		https://togodb.biosciencedbc.jp/togodb/view/genius_orf_list#en

PDB, RefSeq, nr-aa, PROSITE, CATH

PDB structures were assigned to nr-aa protein sequences using PSI-BLAST search. Hit regions which met a similarity threshold calculated using CATH structure information were gathered as intermediate sequences, and genome ORF sequences were assigned to these intermediate sequences by BLAST search. Thus, PDB structures were linked to genome ORF sequences via intermediate sequences.

 817789
Data detail open_in_full
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