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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
Basical information KOME 10.18908/lsdba.nbdc00120-002

Basic Information about full-length cDNA clones

 kome_basical_information.zip
(607 KB) 		http://togodb.biosciencedbc.jp/togodb/view/kome_basical_information#en

The full-length cDNA clones were sequenced by RIKEN and FAIS.

After an all-against-all Blastn search, clones with Expect values less than 1e-180 were grouped into the same cluster.

 37,132 entries
Data detail open_in_full
Blocks search result KOME 10.18908/lsdba.nbdc00120-022

Results of motif searches against the Blocks Database

 kome_blocks_search_result.zip
(60 MB) 		http://togodb.biosciencedbc.jp/togodb/view/kome_blocks_search_result#en

Blocks Database Version 14.0 (October 2003) was used for the searches.

Performed motif searches against the Blocks Database using BLIMPS Version 3.6.

 1,603,600 entries
Data detail open_in_full
GenBank blastn search result KOME 10.18908/lsdba.nbdc00120-007

Results of blastn searches against GenBank nucleotide sequences

 kome_genbank_blastn_search_result.zip
(24 MB) 		http://togodb.biosciencedbc.jp/togodb/view/kome_genbank_blastn_search_result#en

Performed blastn searches against Genbank nucleotide sequences.

Performed homology searches against sequences obtained from NCBI GenBank Release 150.0 (15/08/2005) using the blastn program (blast2.2.12).
Sequences used in the searches were located in the following 10 out of 18 GenBank divisions.
1. PRI - primate sequences
2. ROD - rodent sequences
3. MAM - other mammalian sequences
4. VRT - other vertebrate sequences
5. INV - invertebrate sequences
6. PLN - plant, fungal, and algal sequences
7. BCT - bacterial sequences
8. VRL - viral sequences
9. PHG - bacteriophage sequences
13. PAT - patent sequences
The results are filtered with Expect values lower than 1e-10.

 1,144,403 entries
Data detail open_in_full
GenBank blastx search result KOME 10.18908/lsdba.nbdc00120-008

Results of blastx searches against GenBank amino acid sequences

 kome_genbank_blastx_search_result.zip
(34 MB) 		http://togodb.biosciencedbc.jp/togodb/view/kome_genbank_blastx_search_result#en

Performed blastx searches against Genbank amino acid sequences.

Performed homology searches against sequences obtained from NCBI GenBank Release 150.0 (15/08/2005) using the blastx program (blast2.2.12).
Sequences useed in the searches were located in the following 10 out of 18 GenBank divisions.
1. PRI - primate sequences
2. ROD - rodent sequences
3. MAM - other mammalian sequences
4. VRT - other vertebrate sequences
5. INV - invertebrate sequences
6. PLN - plant, fungal, and algal sequences
7. BCT - bacterial sequences
8. VRL - viral sequences
9. PHG - bacteriophage sequences
13. PAT - patent sequences
The results are filtered with Expect values lower than 1e-10.

 1,247,656 entries
Data detail open_in_full
Genome annotations KOME 10.18908/lsdba.nbdc00120-009

Extracted the hits related to rice genomes from GenBank blastn/blastx results.

 kome_genome_annotation.zip
(514 KB) 		http://togodb.biosciencedbc.jp/togodb/view/kome_genome_annotation#en

Performed blastn searches against Genbank nucleotide sequences and blastx searches against Genbank amino sequences.

Showing the entries related to rice genomes in GenBank blastn/blastx results.
"Related to rice genomes" is defined as follows:
The word "Oryza sativa" or "rice" is included in the definition of the entry and the word "BAC", "PAC", "chromosome Genomic", or "Genomic sequence" is included in the entry.

 23,768 entries
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