# OPDB

**Repository Path**: felixlyd/OPDB

## Basic Information

- **Project Name**: OPDB
- **Description**: OPDB: operon predict database online
- **Primary Language**: Java
- **License**: Apache-2.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2021-10-30
- **Last Updated**: 2021-10-30

## Categories & Tags

**Categories**: Uncategorized

**Tags**: operon

## README

**dependencies:**
___
**basic**
1. [Java 1.6] or later
2. [Python 3.5]
3. [R 3.4.1] or later
4. [kegg] database
5. [NCBI] database
6. [Jbrowse 1.12.3]
7. [samtools 1.6]
8. [rockhopper]
9. [fastq-dump]
10. [deeptools]
11. R library [ProGenome]
12. R library [magrittr]
13. UCSC [wigToBigwig] tools

**Optional**
___
1. [DOOR] database
2. [segemehl]
3. R library [CONDOP]

Thanks!
___
**Result**
![](images/index.png)

the form required your email account to send you a email when your job was done(if the srr_number that you enter is not in our database)

the form required the srr_number and the organism kegg_id

![](images/jbrowse.png)

![](images/igv.png)

[Java 1.6]:http://www.oracle.com/technetwork/java/javase/downloads/index.html

[Python 3.5]:https://www.python.org/downloads/release/python-354/

[R 3.4.1]:https://cran.r-project.org/src/base/R-3/

[kegg]:http://www.genome.jp/kegg/kegg2.html

[NCBI]:https://www.ncbi.nlm.nih.gov/

[Jbrowse 1.12.3]:https://jbrowse.org/install/

[samtools 1.6]:http://samtools.sourceforge.net/

[rockhopper]:https://cs.wellesley.edu/~btjaden/Rockhopper/

[fastq-dump]:https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/

[deeptools]:https://github.com/fidelram/deepTools

[ProGenome]:https://github.com/YulongNiu/ProGenome

[magrittr]:https://github.com/tidyverse/magrittr

[DOOR]:http://csbl.bmb.uga.edu/DOOR/displayNC.php?id=1810

[segemehl]:http://www.bioinf.uni-leipzig.de/Software/segemehl/

[CONDOP]:https://cran.r-project.org/web/packages/CONDOP/index.html

[wigToBigwig]:https://genome.ucsc.edu/goldenpath/help/bigWig.html