TMBETA-GENOME
2015/12/11Web Site: -
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/tmbeta-genome/
The database of transmembrane β-barrel proteins in complete genomes.
README Content
1. Database Component
2. Data Description
2.1 README
| Data name | README |
| Description of data contents | HTML file to describe "TMBETA-GENOME" data. |
| File | README_e.html(English) |
2.2 Sequence Collection
| Data name | Sequence Collection |
| Description of data contents | 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. |
| File | tmbeta_genome_sequence_collection.zip (8.8 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Sequence Collection ID | Sequential serial number assigned to each genome. |
| Classification | Biological classification (Archaea, Bacteria and Eukaryota) |
| Organism Name | Name of the organism. Chromosome number is added to the name if the organism has multiple chromosomes. |
| Locus | RefSeq ID of the genome sequence. |
| FASTA File | Name of the FASTA file where the genome sequence is listed. |
2.3 Sequence Classification
| Data name | Sequence Classification |
| Description of data contents | 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. |
| File | tmbeta_enome_sequence_classification.zip (177 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| Sequence ID | Sequential serial number assigned to each amino acid sequence. |
| Sequence Collection ID | Sequential serial number assigned to each genome. |
| New Approach | Result of predicting transmembrane helical protein using a newly developed method which is performed by the following steps.
|
| SOSUI | Result of predicting transmembrane helical protein using SOSUI. |
| Amino Acid | Result of predicting β-barrel membrane protein with a statistical method using amino acid composition. (TMBETADISC-COMP) |
| Dipeptide | Result of predicting β-barrel membrane protein with a statistical method using residue pair preference. (TMBETADISC_DIPEPTIDE) |
| Motif | Result of predicting β-barrel membrane protein with a statistical method using motifs. (TMBETADISC-MOTIF) |
| SVM | Result of predicting β-barrel membrane protein with a machine learning method using amino acid composition and residue pair preference. (TMBETA-SVM) |
| Header | Header line of the amino acid sequence entry in the FASTA file. |
| Sequence | Amino acid sequence |
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 2.1 Japan.
If you use data from this database, please be sure attribute this database as follows: "TMBETA-GENOME © Michael Gromiha (Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology) licensed under CC Attribution-Share Alike 2.1 Japan".
The summary of the Creative Commons Attribution-Share Alike 2.1 Japan 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 derivative works 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 derivative work.
- You must distribute any derivative work based on part or whole of the data from this database under the license.
- 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.
Dr. M. MICHAEL GROMIHA
Associate Professor
Department of Biotechnology
IIT Madras
Chennai - 600 036
Tel: +91-44-2257-4138(O)
E-mail: gromiha[at]iitm[dot]ac[dot]in
http://www.iitm.ac.in/bioinfo/Gromiha/
4. Update History
| Date | Update contents |
|---|---|
| 2015/12/11 | The following information is updated on the "Database Description" page.
|
| 2015/03/09 | TMBETA-GENOME English archive site is opened. |
5. Literature
Gromiha MM, Yabuki Y, Kundu S, Suharnan S, Suwa M.TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences.
Nucleic Acids Res. 2007 Jan;35(Database issue):D314-6. Epub 2006 Nov 6.
PMID: 17088282
6. Contact address
When you have any question about "TMBETA-GENOME", contact the following:
Dr. M. MICHAEL GROMIHA
Associate Professor
Department of Biotechnology
IIT Madras
Chennai - 600 036
Tel: +91-44-2257-4138(O)
E-mail: gromiha[at]iitm[dot]ac[dot]in
http://www.iitm.ac.in/bioinfo/Gromiha/