License:   msRepDB is a unique resource that can be utilized either as downloadable and an online resource. An institutional license grants full access to both online and downloadable data for all faculty, researchers, staff and students of an academic or nonprofit institution. Please note that this license forbids the use of msRepDB to provide repeat masking or other genome data analysis services to external academic, nonprofit or for-profit customers of the licensed institution. For a license allowing this additional use, please contact us directly. It is recommended to use the chrome browser.

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Online Masking

Function introduction:

1) Users can submit the sequence file in FASTA format to be masked on the “Online Masking” interface by dragging and dropping or paste the sequence to be masked into the input box on the interface;

2) When the server completes the masking task, it will feed back the masking results to the interface, and the user can obtain detailed masking results and related reports by browsing and downloading.


Operation example:

1)Search and select "Drosophila melanogaster" in the list box of species taxonomy name (Only part of the species is displayed in the drop-down box, you can find the interested species by typing in the input box, and the complete species name can be downloaded here ).

2) Download the demo reference genome of Drosophila (Demo Reference Download) to the local disk. The complete Reference download address is (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001215.4);

3) Upload the file "Drosophila_Ref_demo.fna” to the server by dragging and dropping from the online masking interface;
[Server response]: When the server received the submitted file, it will take several to ten minutes to complete masking and generate annotation reports. When the server completes the whole process of online masking, it will prompt that the task has been completed and provide download links for all generated reports.

4) Click the download links in the online masking interface, and save the masked sequence file and several annotation reports to the preferred local directory through the "browse" option.

Diagram of Species Tree

Species Selection Area

Advanced (Optional): online masking parameters

Upload file ready for masking (Do not include special characters such as spaces in filename)



OR

Paste query sequences here:



(Note: To view the results of online masking jobs, click the user name in the upper right corner of the page and select "Online Masking Jobs" in the drop-down box)

Submit

Function introduction:

The submit function is mainly used to update the contents of the database. Update operations can be divided into the following two types.

1) Insert new records;

2) Update existing records in the database;


Operation example:

1) Enter the species' NCBI id, name, and repeat sequence with family information.
[Specific operation]:
Step1: Set the NCBI taxonomy id as “7227”;
Step2: Set the species scientific name as “Drosophila melanogaster”;
Step3: Set the NCBI accession id as “GCA_000001215.4”;
Step4: Set the repeat sequence with family information as
>Node_01#SINE/Alu
GCCGGGCGCGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGAT CGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAG TTCGGCATCAATATGGTGACCTCCCGGGAGCGGGGGACCACCAGGTTGCCTAAGGAGGGG TGAACCGGCCCAGGTCGGAAACGGAGCAGGTCAAAACTCCCGTGCTGATCAGTAGTGGGA TCGCGCCTGTGAATAGCCACTGCACTCCAGCCTGAGCAACATAGCGAGACCCCGTCTCTT
AAAAAAAAAAAAAA

Step4: Click the "Submit" button;

2) Click the "Submit" button on the interface;
[Server response]: When the server received the submitted information, it will take several seconds to complete the storage and generate feedback information on the interface.
Upload file ready for submiting (Do not include special characters such as spaces in filename)



OR

Tools

Function introduction:

The following tools are relevant to our research. If users want to expand the research or verify some results, they can download the tool by clicking the link after the tool name.

Team

Xingyu Liao [First Author], [Project designer]

Postdoctoral Fellow

Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia.


E-mail: xingyu.liao@kaust.edu.sa

Kang Hu [Second Author], [Core developer]

PhD

Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, P.R. China.




E-mail: kanghu@csu.edu.cn

Adil Salhi [Third Author], [Project operation and maintenance personnel]

Research Engineer

Structural and Functional Bioinformatics Group, Postdoctoral Fellows, Knowledge Mining Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia. E-mail: adil.salhi@kaust.edu.sa



E-mail: adil.salhi@kaust.edu.sa

You Zou [Fourth Author], [Project operation and maintenance personnel]

Ph.D. Student, Research Engineer

High Performance Computing Center, Central South University, Changsha 410083, P.R. China.


E-mail: zouyou@csu.edu.cn

Jianxin Wang [Corresponding Author], [Project manager]

Professor and Dean

Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, P.R. China.


E-mail: jxwang@mail.csu.edu.cn

Xin Gao [Corresponding Author], [Project manager]

Professor, Computer Science

Principal Investigator, Structural and Functional Bioinformatics Group, Acting Associate Director, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia.


E-mail: xin.gao@kaust.edu.sa