GENIUS II
2017/10/11Web Site: （Closed）http://genius.cbrc.jp
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/genius/
The database in which protein coding regions in genomes are assigned to three-dimensional structures.
README Content
1. Database Component
2. Data Description
2.1 README
| Data name | README |
|---|---|
| Description of data contents | HTML file to describe "GENIUS II" data. |
| File | README_e.html (English) |
2.2 HTML Source
| Data name | HTML Source |
|---|---|
| Description of data contents | HTML Source of the original site (terminated). Note that links to CGI don't work. |
| File | HTML_Source.tar.gz (41MB) |
2.3 ORF List
| Data name | ORF List |
|---|---|
| Description of data contents | This is the ORF list of 234 genomes. You can access to ORF sequences and these alignments information. |
| File | genius_orf_list.zip (15 MB)
Analysis_Result.tar.gz (28 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| ORF Name | ORF Name |
| ORF ID | ORF ID |
| Superkingdom | Superkingdom of the species which contains this ORF |
| Species | The species which contains this ORF |
| Chromosome | The chromosome (Refseq ID) which contains this ORF |
| Alignment (PDB & Intermediate Sequence) | PDB ID and its corresponding intermediate sequence ID It links to the alignment information. |
| Alignment (ORF & Intermediate Sequence) | ORF Name and its corresponding intermediate sequence ID It links to the alignment information. |
| Region in PDB (3D) | The position of PDB 3D structure corresponding this ORF |
| Prosite Motifs (in ORF)(in PDB) | The PROSITE motif corresponding this ORF |
2.4 ORF Sequence
| Data name | ORF Sequence |
|---|---|
| Description of data contents | ORF sequence (amino acid) |
| File | genius_orf_sequence.zip (164 MB)
ORF_Sequence.tar.gz (182 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| Chromosome | The chromosome (Refseq ID) which contains this ORF |
| ORF ID | ORF ID |
| Header | FASTA header of this sequence |
| Sequence | Sequence |
2.5 PDB Alignment
| Data name | PDB Alignment |
|---|---|
| Description of data contents | It links to the PSI-BLAST alingment information between PDB and intermediate sequences |
| File | genius_pdb_alignment.zip (23 KB)
PDB_Alignment.tar.gz (4.3 GB) |
Data items are the following:
| Data item | Description |
|---|---|
| Query | PSI-BLAST search query (PDB ID) |
| Alignment | It links to the alignment result file. |
2.6 ORF Alignment
| Data name | ORF Alignment |
|---|---|
| Description of data contents | It links to the alingment information between ORF and intermediate sequences |
| File | genius_orf_alignment.zip (170 MB)
ORF_Alignment.tar.gz (168 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| Chromosome | The chromosome (RefSeq ID) which contains this ORF |
| Query | BLAST search query (ORF ID) |
| Alignment | Alignment result |
3. License
You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.
The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "GENIUS II c Suwa Makiko (Aoyama Gakuin University) licensed under CC Attribution-Share Alike 4.0 International".
The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.
With regard to this database, you are licensed to:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- freely create and distribute database and other adapted materials based on part or whole of the data from this database,
under the license, as long as you comply with the following conditions:
- You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
- You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
- You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.
Suwa Makiko
E-mail: suwa[at]chem[dot]aoyama[dot]ac[dot]jp
4. Update History
| Date | Update contents |
|---|---|
| 2017/10/11 | GENIUS II English archive site is opened. |
| - | GENIUS II(http://genius.cbrc.jp) is opened. |
5. Literature
Yabuki, Y., Mukai, Y., Swindells, M. B. and Suwa M.GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structures
Bioinformatics (2004), 20 :596-598.
PMID: 14751990